GPF Documentation
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GPF Documentation
Index
Index
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D
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E
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F
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G
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H
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I
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J
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O
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P
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U
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V
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W
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X
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Y
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Z
A
AbstractDuckDbImportStorage (class in gpf.duckdb_storage.duckdb_import_storage)
AbstractDuckDbStorage (class in gpf.duckdb_storage.duckdb_genotype_storage)
AbstractRunner (class in gpf.tools.gpf_validation_runner)
acgt_gpf() (in module gpf.testing.acgt_import)
adapt() (gpf.query_variants.query_runners.QueryRunner method)
add_argparser_arguments() (gpf.genotype_storage.genotype_storage_genomic_context_cli.CLIGenotypeStorageContextProvider method)
(gpf.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceContextProvider method)
add_arguments() (gpf.gpf_instance.adjustments.adjust_duckdb_storage.AdjustDuckDbStorageCommand static method)
(gpf.gpf_instance.adjustments.adjust_impala_storage.AdjustImpalaStorageCommand static method)
(users_api.management.commands.user_set_name.Command method)
(users_api.management.commands.user_setpasswd.Command method)
(users_api.management.commands.users_remove.Command method)
add_gene() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method)
add_measure_task() (gpf.pheno.prepare_data.PreparePhenoBrowserBase method)
add_members() (gpf.pedigrees.family.Family method)
add_missing_members() (gpf.pedigrees.pedigrees.FamilyConnections static method)
add_missing_parquet_fields() (in module gpf.parquet.parquet_writer)
add_page() (gpf.pedigrees.drawing.PDFLayoutDrawer method)
add_parent() (gpf.studies.study.GenotypeData method)
add_pheno_common_inference() (in module gpf.pheno.pheno_import)
add_rank() (gpf.pedigrees.pedigrees.Individual method)
add_ranks() (gpf.pedigrees.pedigrees.FamilyConnections method)
add_tagger() (gpf.pedigrees.family_tag_builder.FamilyTagsBuilder method)
add_to_parser() (gpf.variants_loaders.raw.loader.CLIArgument method)
add_unnest_in_join() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method)
(gpf.query_variants.sql.schema2.base_query_builder.Dialect static method)
add_variant_count() (in module gpf.gene_profile.generate_gene_profile)
adjust_chrom_prefix() (in module gpf.variants_loaders.raw.flexible_variant_loader)
adjust_dataset() (gpf.gpf_instance.adjustments.gpf_instance_adjustments.EnableDisableStudies method)
(gpf.gpf_instance.adjustments.gpf_instance_adjustments.StudyConfigsAdjustmentCommand method)
adjust_study() (gpf.gpf_instance.adjustments.gpf_instance_adjustments.DefaultGenotypeStorage method)
(gpf.gpf_instance.adjustments.gpf_instance_adjustments.EnableDisableStudies method)
(gpf.gpf_instance.adjustments.gpf_instance_adjustments.StudyConfigsAdjustmentCommand method)
AdjustDuckDbStorageCommand (class in gpf.gpf_instance.adjustments.adjust_duckdb_storage)
AdjustImpalaStorageCommand (class in gpf.gpf_instance.adjustments.adjust_impala_storage)
AdjustmentsCommand (class in gpf.gpf_instance.adjustments.adjust_command)
affected (gpf.variants.attributes.Status attribute)
AFFECTED_DAD (gpf.pedigrees.family.FamilyTag attribute)
AFFECTED_MOM (gpf.pedigrees.family.FamilyTag attribute)
AFFECTED_PRB (gpf.pedigrees.family.FamilyTag attribute)
AFFECTED_SIB (gpf.pedigrees.family.FamilyTag attribute)
affected_statues (gpf.studies.study.PSCQueryAdjustments attribute)
aliases() (gpf.variants.attributes.Sex static method)
align_na_results() (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapter static method)
(pheno_tool_api.adapter.PhenoToolAdapter static method)
all (gpf.enrichment_tool.event_counters.EnrichmentResult attribute)
(gpf.enrichment_tool.event_counters.EventCountersResult attribute)
(gpf.enrichment_tool.event_counters.EventsResult attribute)
(gpf.enrichment_tool.event_counters.VariantEventsResult attribute)
all() (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method)
(gpf.query_variants.attribute_queries.SyntaxSugarTransformer method)
all_count() (gpf.pheno.graphs.GraphColumn method)
all_labels() (gpf.pedigrees.family.FamilyTag static method)
all_region_bins() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method)
all_tag_labels() (gpf.pedigrees.family.Person method)
all_tags() (gpf.pedigrees.family.FamilyTag static method)
alla_gpf() (in module gpf.testing.alla_import)
Allele (class in gpf.variants.core)
Allele.Type (class in gpf.variants.core)
allele_count (gpf.variants.family_variant.FamilyVariant property)
(gpf.variants.variant.SummaryVariant property)
allele_events (gpf.enrichment_tool.genotype_helper.VariantEvent attribute)
allele_in_members (gpf.variants.family_variant.FamilyAllele property)
allele_in_roles (gpf.variants.family_variant.FamilyAllele property)
allele_in_sexes (gpf.variants.family_variant.FamilyAllele property)
allele_in_statuses (gpf.variants.family_variant.FamilyAllele property)
allele_index (gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.variant.SummaryAllele property)
allele_indexes (gpf.variants.family_variant.FamilyVariant property)
allele_type (gpf.variants.core.Allele property)
(gpf.variants.family_variant.FamilyAllele property)
allele_type_from_cshl_variant() (in module gpf.variants.variant)
allele_type_from_name() (in module gpf.variants.variant)
AlleleEvent (class in gpf.enrichment_tool.genotype_helper)
AlleleParquetSerializer (class in gpf.parquet.schema2.serializers)
alleles (gpf.variants.family_variant.FamilyVariant property)
(gpf.variants.variant.SummaryVariant property)
alt_alleles (gpf.variants.variant.SummaryVariant property)
alternative (gpf.variants.core.Allele property)
(gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.variant.SummaryVariant property)
and_() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method)
(gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method)
(gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method)
annotation_schema (gpf.variants_loaders.raw.loader.VariantsLoader property)
(gpf.variants_loaders.raw.loader.VariantsLoaderDecorator property)
AnnotationPipelineVariantsBatchFilter (class in gpf.parquet.schema2.processing_pipeline)
AnnotationPipelineVariantsFilter (class in gpf.parquet.schema2.processing_pipeline)
AnnotationPipelineVariantsFilterMixin (class in gpf.parquet.schema2.processing_pipeline)
any() (gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method)
(gpf.query_variants.attribute_queries.SyntaxSugarTransformer method)
append() (gpf.tools.gpf_validation_runner.TestSuite method)
append_allele() (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method)
(gpf.parquet.schema2.variants_parquet_writer.ContinuousParquetFileWriter method)
append_meta_to_parquet() (in module gpf.parquet.parquet_writer)
apply() (gpf.person_filters.FamilyFilter method)
(gpf.person_filters.person_filters.CriteriaFilter method)
(gpf.person_filters.person_filters.FamilyFilter method)
(gpf.person_filters.person_filters.PersonFilter method)
(gpf.person_filters.person_filters.PhenoFilter method)
(gpf.person_filters.PersonFilter method)
(gpf.person_filters.PhenoFilter method)
apply_family_heuristics() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method)
apply_mask() (gpf.utils.variant_utils.BitmaskEnumTranslator method)
apply_summary_heuristics() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method)
apply_to_df() (gpf.person_filters.FamilyFilter method)
(gpf.person_filters.person_filters.FamilyFilter method)
(gpf.person_filters.person_filters.PersonFilter method)
(gpf.person_filters.person_filters.PersonFilterRange method)
(gpf.person_filters.person_filters.PersonFilterSet method)
(gpf.person_filters.PersonFilter method)
(gpf.person_filters.PersonFilterRange method)
(gpf.person_filters.PersonFilterSet method)
apply_to_family() (gpf.pedigrees.layout.Layout method)
are_mates() (gpf.pedigrees.pedigrees.Individual method)
are_siblings() (gpf.pedigrees.pedigrees.Individual method)
ARGUMENT (gpf.variants_loaders.raw.loader.ArgumentType attribute)
ArgumentType (class in gpf.variants_loaders.raw.loader)
array_item_suffix() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method)
(gpf.query_variants.sql.schema2.base_query_builder.Dialect static method)
AttributeQueriesUnsupportedException
AttributeQueryNotSupported
AttributeQueryTransformer (class in gpf.query_variants.attribute_queries)
AttributeQueryTransformerFunction (class in gpf.query_variants.attribute_queries)
AttributeQueryTransformerSQL (class in gpf.query_variants.attribute_queries)
AttributeQueryTransformerSQLLegacy (class in gpf.query_variants.attribute_queries)
attributes (gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.variant.SummaryAllele property)
(gpf.variants.variant.SummaryVariant property)
authenticate() (utils.authentication.GPFOAuth2Authentication method)
(utils.authentication.ReadOnlyDBAuthentication method)
(utils.authentication.SessionAuthenticationWithUnauthenticatedCSRF method)
autosomal (gpf.variants.attributes.GeneticModel attribute)
autosomal_broken (gpf.variants.attributes.GeneticModel attribute)
B
backend (gpf.studies.study.GenotypeDataStudy property)
background_id (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property)
(gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property)
background_type (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property)
(gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property)
backup_schema2_study() (in module gpf.parquet.schema2.annotate_schema2_parquet)
base_dir (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute)
(gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute)
BaseCommonReportsHelper (class in common_reports_api.common_reports_helper)
BaseEnrichmentBackground (class in gpf.enrichment_tool.base_enrichment_background)
BaseEnrichmentBuilder (class in enrichment_api.enrichment_builder)
BaseEnrichmentHelper (class in enrichment_api.enrichment_helper)
BaseEnrichmentResourceBackground (class in gpf.enrichment_tool.base_enrichment_background)
BaseGenotypeBrowserRunner (class in gpf.tools.gpf_validation_runner)
BasePhenoBrowserHelper (class in pheno_browser_api.pheno_browser_helper)
BaseQueryBuilder (class in gpf.query_variants.sql.schema2.base_query_builder)
BATCH_ROWS (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter attribute)
BATCH_SIZE (gpf.schema2_storage.schema2_import_storage.Schema2ImportStorage attribute)
best2gt() (in module gpf.utils.variant_utils)
best_st (gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
best_state (gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
bitmask2inheritance() (in module gpf.variants.attributes)
BitmaskEnumTranslator (class in gpf.utils.variant_utils)
blob_column() (gpf.parquet.schema2.serializers.AlleleParquetSerializer method)
(gpf.parquet.schema2.serializers.FamilyAlleleParquetSerializer method)
(gpf.parquet.schema2.serializers.SummaryAlleleParquetSerializer method)
bold_red (gpf_web.default_settings.CustomFormatter attribute)
broken_families (gpf.pedigrees.families_data.FamiliesData property)
browsable_figure_path() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method)
browser (gpf.pheno.pheno_data.PhenotypeData property)
Bucket (class in gpf.import_tools.import_tools)
bucket_url (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute)
build() (enrichment_api.enrichment_builder.EnrichmentBuilder method)
(gpf.gpf_instance.gpf_instance.GPFInstance static method)
(gpf.gpf_instance.GPFInstance static method)
(gpf.pheno.graphs.GraphColumn static method)
(gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
build_allele_record_dict() (gpf.parquet.schema2.serializers.AlleleParquetSerializer method)
(gpf.parquet.schema2.serializers.FamilyAlleleParquetSerializer method)
(gpf.parquet.schema2.serializers.SummaryAlleleParquetSerializer method)
build_and_save() (gpf.pheno.pheno_data.PhenotypeData method)
(gpf.studies.study.GenotypeData method)
build_annotation_filename() (in module gpf.inmemory_storage.annotation_serialization)
build_annotation_pipeline() (gpf.import_tools.import_tools.ImportProject method)
build_arguments_dict() (gpf.variants_loaders.raw.loader.CLILoader method)
(gpf.variants_loaders.raw.loader.VariantsLoaderDecorator method)
build_array_join() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect method)
(gpf.query_variants.sql.schema2.base_query_builder.Dialect method)
build_backend() (gpf.genotype_storage.genotype_storage.GenotypeStorage method)
build_batch() (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method)
build_blob_schema() (gpf.parquet.schema2.serializers.SummaryAlleleParquetSerializer class method)
build_cache() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method)
build_cli_arguments() (gpf.variants_loaders.raw.loader.CLILoader class method)
(gpf.variants_loaders.raw.loader.VariantsLoaderDecorator class method)
build_cli_arguments_parser() (gpf.tools.liftover_tools.CNVLiftoverTool method)
(gpf.tools.liftover_tools.DaeLiftoverTool method)
(gpf.tools.liftover_tools.DenovoLiftoverTool method)
(gpf.tools.liftover_tools.LiftoverTool method)
(gpf.tools.liftover_tools.VCFLiftoverTool method)
build_cnv_allele() (gpf.variants.core.Allele static method)
build_coding_length_background() (in module gpf.enrichment_tool.build_coding_length_enrichment_background)
build_collection() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection static method)
(gpf.gene_sets.denovo_gene_set_helpers.DenovoGeneSetHelpers class method)
build_config() (gpf.configuration.study_config_builder.StudyConfigBuilder method)
build_configuration() (gpf.gene_profile.db.GeneProfileDBWriter class method)
build_enrichment_event_counts_cache() (in module gpf.enrichment_tool.enrichment_cache_builder)
build_families_data() (in module gpf.pedigrees.testing)
build_families_data_from_pedigree() (gpf.pedigrees.loader.FamiliesLoader static method)
build_families_report() (in module gpf.tools.draw_pedigree)
build_family() (in module gpf.pedigrees.testing)
build_family_layout() (in module gpf.tools.draw_pedigree)
build_family_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
build_family_schema() (in module gpf.parquet.schema2.serializers)
build_family_variants_query() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method)
build_family_variants_query_runner() (gpf.duckdb_storage.duckdb2_variants.DuckDb2Variants method)
(gpf.inmemory_storage.raw_variants.RawFamilyVariants method)
(gpf.parquet_storage.storage.ParquetLoaderVariants method)
(gpf.query_variants.base_query_variants.QueryVariants method)
(gpf.query_variants.sql.schema2.base_variants.SqlSchema2Variants method)
build_from_config() (gpf.import_tools.import_tools.ImportProject static method)
build_from_file() (gpf.import_tools.import_tools.ImportProject static method)
build_gene_regions() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method)
build_gene_weights_enrichment_background() (in module gpf.enrichment_tool.resource_implementations.enrichment_resource_impl)
build_genomic_scores_registry() (gpf.genomic_scores.scores.GenomicScoresRegistry static method)
build_genotype_data_all_datasets() (studies.study_wrapper.WDAEStudy static method)
build_genotype_data_description() (studies.study_wrapper.WDAEAbstractStudy method)
(studies.study_wrapper.WDAEStudy method)
build_id() (gpf.pedigrees.family_role_builder.Mating static method)
build_import_project() (in module gpf.tools.simple_study_import)
build_liftover_pipeline() (gpf.tools.liftover_tools.LiftoverTool method)
build_option() (gpf.variants_loaders.raw.loader.CLIArgument method)
build_partitions() (in module gpf.gene_profile.generate_gene_profile)
build_pheno_browser() (in module gpf.pheno.build_pheno_browser)
build_phenotype_study() (gpf.pheno.storage.PhenotypeStorage method)
build_position_allele() (gpf.variants.core.Allele static method)
build_query() (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder method)
build_rare_query() (in module gpf.gene_profile.generate_gene_profile)
build_regression() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method)
build_report() (gpf.pheno.pheno_data.PhenotypeData method)
(gpf.studies.study.GenotypeData method)
build_report_description() (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method)
(pheno_tool_api.adapter.PhenoToolAdapter method)
build_results() (enrichment_api.enrichment_builder.EnrichmentBuilder method)
build_roles() (gpf.pedigrees.family_role_builder.FamilyRoleBuilder method)
build_samocha_enrichment_background() (in module gpf.enrichment_tool.resource_implementations.enrichment_resource_impl)
build_schema() (gpf.parquet.schema2.serializers.FamilyAlleleParquetSerializer class method)
(gpf.parquet.schema2.serializers.SummaryAlleleParquetSerializer class method)
(gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method)
build_serializer() (gpf.parquet.schema2.serializers.VariantsDataSerializer static method)
build_study_layout() (gpf.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method)
(gpf.duckdb_storage.duckdb_genotype_storage.DuckDbParquetStorage method)
(gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3ParquetStorage method)
(gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage method)
(gpf.duckdb_storage.duckdb_genotype_storage.DuckDbStorage method)
build_summary_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
build_summary_schema() (in module gpf.parquet.schema2.serializers)
build_summary_variants_query() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method)
build_summary_variants_query_runner() (gpf.duckdb_storage.duckdb2_variants.DuckDb2Variants method)
(gpf.inmemory_storage.raw_variants.RawFamilyVariants method)
(gpf.parquet_storage.storage.ParquetLoaderVariants method)
(gpf.query_variants.base_query_variants.QueryVariants method)
(gpf.query_variants.sql.schema2.base_variants.SqlSchema2Variants method)
build_table() (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method)
build_table_name() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect method)
(gpf.query_variants.sql.schema2.base_query_builder.Dialect method)
build_values_categorical_distribution() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method)
build_values_ordinal_distribution() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method)
build_values_violinplot() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method)
build_variant_row() (studies.response_transformer.ResponseTransformer method)
(studies.study_wrapper.ResponseTransformerProtocol method)
build_variant_types_query() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method)
build_vcf_allele() (gpf.variants.core.Allele static method)
C
CACHE_LOCK (gpf.pheno.registry.PhenoRegistry attribute)
calc() (gpf.pheno_tool.tool.PhenoTool method)
calc_alleles() (gpf.variants.family_variant.FamilyVariant static method)
calc_alt_alleles() (gpf.variants.family_variant.FamilyVariant static method)
calc_batched_heuristics() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method)
calc_by_effect() (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method)
(gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapterBase method)
(pheno_tool_api.adapter.PhenoToolAdapter method)
calc_coding_bins() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method)
calc_enrichment_test() (enrichment_api.enrichment_helper.EnrichmentHelper method)
(gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground method)
(gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method)
(gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method)
(gpf.enrichment_tool.samocha_background.SamochaEnrichmentBackground method)
calc_expected_observed_pvalue() (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground static method)
(gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground static method)
calc_family_bins() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method)
calc_frequency_bins() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method)
calc_heuristics() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method)
calc_info_hash() (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method)
calc_inheritance_trio() (gpf.variants.family_variant.FamilyAllele class method)
calc_region_bins() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method)
calc_regression() (gpf.pheno.utils.lin_regress.LinearRegression method)
calc_statistics_hash() (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method)
calc_variants() (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method)
(gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapterBase method)
(pheno_tool_api.adapter.PhenoToolAdapter method)
(pheno_tool_api.adapter.PhenoToolAdapterBase method)
calculate_simple_best_state() (in module gpf.variants.family_variant)
can_extend() (gpf.pedigrees.pedigrees.Realization method)
categorical (gpf.pheno.common.InferenceConfig attribute)
(gpf.pheno.common.MeasureType attribute)
categorical_attr() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
categorical_config (gpf.pheno.common.MeasureHistogramConfigs attribute)
check_affected_dad_family() (in module gpf.pedigrees.family_tag_builder)
check_affected_mom_family() (in module gpf.pedigrees.family_tag_builder)
check_affected_prb_family() (in module gpf.pedigrees.family_tag_builder)
check_affected_sib_family() (in module gpf.pedigrees.family_tag_builder)
check_control_family() (in module gpf.pedigrees.family_tag_builder)
check_denovo_trio() (gpf.variants.family_variant.FamilyAllele static method)
CHECK_DONE_VERBOSITY (gpf.query_variants.query_runners.QueryResult attribute)
check_family_tags_query() (in module gpf.pedigrees.family_tag_builder)
check_female_prb_family() (in module gpf.pedigrees.family_tag_builder)
check_inheritance_denovo_only() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method)
check_inheritance_query_value() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method)
check_male_prb_family() (in module gpf.pedigrees.family_tag_builder)
check_mendelian_trio() (gpf.variants.family_variant.FamilyAllele static method)
check_missing_dad_family() (in module gpf.pedigrees.family_tag_builder)
check_missing_mom_family() (in module gpf.pedigrees.family_tag_builder)
check_multiplex_family() (in module gpf.pedigrees.family_tag_builder)
check_nuclear_family() (in module gpf.pedigrees.family_tag_builder)
check_omission_trio() (gpf.variants.family_variant.FamilyAllele static method)
check_quad_family() (in module gpf.pedigrees.family_tag_builder)
check_roles_denovo_only() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method)
check_roles_query_value() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method)
check_simplex_family() (in module gpf.pedigrees.family_tag_builder)
check_tag() (in module gpf.pedigrees.family_tag_builder)
check_trio_family() (in module gpf.pedigrees.family_tag_builder)
check_unaffected_dad_family() (in module gpf.pedigrees.family_tag_builder)
check_unaffected_mom_family() (in module gpf.pedigrees.family_tag_builder)
check_unaffected_prb_family() (in module gpf.pedigrees.family_tag_builder)
check_unaffected_sib_family() (in module gpf.pedigrees.family_tag_builder)
check_variant_types_value() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase static method)
checkers (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute)
child (gpf.variants.attributes.Role attribute)
children_set() (gpf.pedigrees.pedigrees.Individual method)
(gpf.pedigrees.pedigrees.IndividualGroup method)
(gpf.pedigrees.pedigrees.MatingUnit method)
(gpf.pedigrees.pedigrees.SibshipUnit method)
children_zygosity (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute)
ChildrenBySex (class in gpf.person_sets)
(class in gpf.person_sets.person_sets)
ChildrenStats (class in gpf.person_sets)
(class in gpf.person_sets.person_sets)
chrom (gpf.variants.core.Allele property)
(gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
(gpf.variants.variant.SummaryVariant property)
chromosome (gpf.variants.core.Allele property)
(gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
(gpf.variants.variant.SummaryVariant property)
chromosomes (gpf.variants_loaders.cnv.loader.CNVLoader property)
(gpf.variants_loaders.dae.loader.DaeTransmittedLoader property)
(gpf.variants_loaders.dae.loader.DenovoLoader property)
(gpf.variants_loaders.parquet.loader.ParquetLoader property)
(gpf.variants_loaders.raw.loader.VariantsLoader property)
(gpf.variants_loaders.raw.loader.VariantsLoaderDecorator property)
(gpf.variants_loaders.vcf.loader.SingleVcfLoader property)
(gpf.variants_loaders.vcf.loader.VcfLoader property)
clear_tags() (gpf.pedigrees.family_tag_builder.FamilyTagsBuilder method)
cli() (in module gpf.enrichment_tool.build_coding_length_enrichment_background)
(in module gpf.enrichment_tool.build_ur_synonymous_enrichment_background)
(in module gpf.enrichment_tool.enrichment_cache_builder)
(in module gpf.gpf_instance.adjustments.gpf_instance_adjustments)
(in module gpf.parquet.schema2.annotate_schema2_parquet)
(in module gpf.tools.reannotate_instance)
(in module gpf_web.wgpf)
cli_arguments() (gpf.variants_loaders.raw.loader.CLILoader class method)
(gpf.variants_loaders.raw.loader.VariantsLoaderDecorator class method)
(in module gpf.tools.simple_study_import)
cli_cache_repo() (in module gpf.tools.grr_cache_repo)
cli_defaults() (gpf.variants_loaders.raw.loader.CLILoader class method)
(gpf.variants_loaders.raw.loader.VariantsLoaderDecorator class method)
cli_export() (in module gpf.gene_profile.exporter)
CLIArgument (class in gpf.variants_loaders.raw.loader)
CLIGenotypeStorageContextProvider (class in gpf.genotype_storage.genotype_storage_genomic_context_cli)
CLILoader (class in gpf.variants_loaders.raw.loader)
close() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method)
(gpf.gpf_instance.adjustments.adjust_command.AdjustmentsCommand method)
(gpf.parquet.schema2.loader.MultiReader method)
(gpf.parquet.schema2.loader.Reader method)
(gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method)
(gpf.parquet.schema2.variants_parquet_writer.ContinuousParquetFileWriter method)
(gpf.parquet.schema2.variants_parquet_writer.VariantsParquetWriter method)
(gpf.pedigrees.families_data.FamiliesData method)
(gpf.pheno.browser.PhenoBrowser method)
(gpf.pheno.pheno_data.PhenotypeData method)
(gpf.pheno.prepare_data.PreparePhenoBrowserBase method)
(gpf.query_variants.query_runners.QueryResult method)
(gpf.query_variants.query_runners.QueryRunner method)
(gpf.studies.study.GenotypeData method)
(gpf.variants_loaders.cnv.loader.CNVLoader method)
(gpf.variants_loaders.dae.loader.DaeTransmittedLoader method)
(gpf.variants_loaders.dae.loader.DenovoLoader method)
(gpf.variants_loaders.parquet.loader.ParquetLoader method)
(gpf.variants_loaders.raw.loader.VariantsLoader method)
(gpf.variants_loaders.raw.loader.VariantsLoaderDecorator method)
(gpf.variants_loaders.vcf.loader.SingleVcfLoader method)
(gpf.variants_loaders.vcf.loader.VcfLoader method)
(gpf.variants_loaders.vcf.serializer.VcfSerializer method)
cnv (gpf.testing.import_helpers.StudyInputLayout attribute)
(gpf.variants.core.Allele.Type attribute)
cnv_import() (in module gpf.testing.import_helpers)
cnv_liftover_main() (in module gpf.tools.liftover_tools)
cnv_study() (in module gpf.testing.import_helpers)
CNVLiftoverTool (class in gpf.tools.liftover_tools)
CNVLoader (class in gpf.variants_loaders.cnv.loader)
coding_bin (gpf.parquet.partition_descriptor.Partition attribute)
coding_bins (gpf.query_variants.sql.schema2.sql_query_builder.QueryHeuristics attribute)
coding_bins() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
coding_len_background() (in module enrichment_api.tests.conftest)
coercers (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute)
collect_child_configs() (gpf.pheno.prepare_data.PreparePhenoBrowserBase method)
collect_denovo_events() (gpf.enrichment_tool.genotype_helper.GenotypeHelper static method)
collect_directory_configs() (gpf.configuration.gpf_config_parser.GPFConfigParser class method)
collect_expectations() (gpf.tools.gpf_validation_runner.MainRunner static method)
collect_genotype_data_backgrounds() (enrichment_api.enrichment_helper.EnrichmentHelper method)
collect_instruments() (in module gpf.pheno.pheno_import)
collect_pedigree_parquet_schema() (in module gpf.parquet.parquet_writer)
collect_person_collection_attributes() (gpf.person_sets.person_sets.PersonSetCollection method)
(gpf.person_sets.PersonSetCollection method)
collect_variant_counts() (in module gpf.gene_profile.generate_gene_profile)
collections_descriptions (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb property)
(gpf.gene_sets.gene_sets_db.GeneSetsDb property)
color (gpf.person_sets.person_sets.PersonSetConfig attribute)
(gpf.person_sets.PersonSetConfig attribute)
column_counts() (in module gpf.pheno.graphs)
column_name (gpf.common_reports.denovo_report.EffectCell property)
combine() (gpf.pedigrees.families_data.FamiliesData static method)
(gpf.person_sets.person_sets.PersonSetCollection static method)
(gpf.person_sets.PersonSetCollection static method)
(gpf.variants.variant.VariantDesc static method)
Command (class in users_api.management.commands.user_set_name)
(class in users_api.management.commands.user_setpasswd)
(class in users_api.management.commands.users_remove)
common_report (gpf.pheno.common.StudyConfig attribute)
common_reports_api
module
common_reports_api.common_reports_helper
module
common_reports_api.tests
module
common_reports_api.tests.test_common_reports_api
module
CommonReport (class in gpf.common_reports.common_report)
CommonReportsHelper (class in common_reports_api.common_reports_helper)
CommonStudyMixin (class in gpf.studies.study)
complex (gpf.variants.core.Allele.Type attribute)
compound() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method)
(gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method)
(gpf.query_variants.attribute_queries.AttributeQueryTransformerSQLLegacy method)
(gpf.query_variants.attribute_queries.CompoundStripTransformer method)
(gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method)
CompoundStripTransformer (class in gpf.query_variants.attribute_queries)
config (studies.study_wrapper.WDAEAbstractStudy property)
config_columns (studies.study_wrapper.WDAEAbstractStudy property)
config_json() (gpf.person_sets.person_sets.PersonSetCollection method)
(gpf.person_sets.PersonSetCollection method)
ConfigDumper (class in gpf.configuration.study_config_builder)
connect() (gpf.duckdb_storage.duckdb_connection_factory.DuckDbConnectionFactory method)
(gpf.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method)
(gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method)
connected_components() (gpf.pedigrees.pedigrees.FamilyConnections method)
construct_import_annotation_pipeline() (in module gpf.import_tools.import_tools)
construct_import_annotation_pipeline_config() (in module gpf.import_tools.import_tools)
continuous (gpf.pheno.common.InferenceConfig attribute)
(gpf.pheno.common.MeasureType attribute)
ContinuousParquetFileWriter (class in gpf.parquet.schema2.parquet_io)
(class in gpf.parquet.schema2.variants_parquet_writer)
CONTROL (gpf.pedigrees.family.FamilyTag attribute)
convert() (in module utils.streaming_response_util)
convert_to_float() (in module gpf.pheno.prepare.measure_classifier)
convert_to_int() (in module gpf.pheno.prepare.measure_classifier)
convert_to_numeric() (in module gpf.pheno.prepare.measure_classifier)
convert_to_string() (in module gpf.pheno.prepare.measure_classifier)
Convertible (class in gpf.pheno.prepare.measure_classifier)
copy() (gpf.pedigrees.families_data.FamiliesData method)
(gpf.pedigrees.pedigrees.Realization method)
copy_graph() (in module gpf.pedigrees.pedigrees)
count_measures() (gpf.pheno.browser.PhenoBrowser method)
(gpf.pheno.pheno_data.PhenotypeData method)
(gpf.pheno.pheno_data.PhenotypeGroup method)
(gpf.pheno.pheno_data.PhenotypeStudy method)
count_total (gpf.pheno.prepare.measure_classifier.InferenceReport attribute)
count_unique_values (gpf.pheno.prepare.measure_classifier.InferenceReport attribute)
count_variant() (gpf.common_reports.denovo_report.EffectCell method)
(gpf.common_reports.denovo_report.EffectRow method)
(in module gpf.gene_profile.generate_gene_profile)
count_with_values (gpf.pheno.prepare.measure_classifier.InferenceReport attribute)
count_without_values (gpf.pheno.prepare.measure_classifier.InferenceReport attribute)
counter() (gpf.tools.gpf_validation_runner.AbstractRunner method)
(gpf.tools.gpf_validation_runner.MainRunner method)
CounterBase (class in gpf.enrichment_tool.event_counters)
CountError
create_and_node() (in module gpf.query_variants.attribute_queries)
create_background() (enrichment_api.enrichment_helper.EnrichmentHelper method)
create_browser() (gpf.pheno.pheno_data.PhenotypeData static method)
create_browser_tables() (gpf.pheno.browser.PhenoBrowser static method)
create_counter() (enrichment_api.enrichment_helper.EnrichmentHelper method)
create_database_connection() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method)
(in module gpf.duckdb_storage.duckdb_storage_helpers)
create_denovo_gene_set_spec() (in module gpf.gene_sets.denovo_gene_sets_config)
create_df() (gpf.pheno_tool.tool.PhenoTool method)
create_duckdb_tables() (in module gpf.duckdb_storage.duckdb_storage_helpers)
create_empty_collection() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection static method)
create_enrichment_description() (enrichment_api.enrichment_builder.EnrichmentBuilder method)
create_gp_table() (gpf.gene_profile.db.GeneProfileDBWriter method)
create_import_tasks() (in module gpf.pheno.pheno_import)
create_memory_connection() (in module gpf.duckdb_storage.duckdb_storage_helpers)
create_or_node() (in module gpf.query_variants.attribute_queries)
create_parquet_scans_layout_from_layout() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage static method)
create_parquet_scans_layout_relative() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method)
create_reference_allele() (gpf.variants.variant.SummaryAllele static method)
create_relative_parquet_scans_layout() (in module gpf.duckdb_storage.duckdb_storage_helpers)
create_runner() (gpf.genotype_storage.genotype_storage.GenotypeStorage method)
create_s3_attach_db_clause() (in module gpf.duckdb_storage.duckdb_storage_helpers)
create_s3_filesystem() (in module gpf.duckdb_storage.duckdb_storage_helpers)
create_s3_secret_clause() (in module gpf.duckdb_storage.duckdb_storage_helpers)
create_sandwich_instance() (gpf.pedigrees.pedigrees.FamilyConnections method)
create_schema2_dataset_layout() (in module gpf.schema2_storage.schema2_layout)
create_statistics_build_tasks() (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method)
create_study_parquet_tables_layout() (in module gpf.duckdb_storage.duckdb_storage_helpers)
create_summary_runner() (gpf.genotype_storage.genotype_storage.GenotypeStorage method)
create_table() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method)
(gpf.pheno.common.ImportManifest static method)
create_table_layout() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage static method)
(in module gpf.duckdb_storage.duckdb_storage_helpers)
create_table_partitioned() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method)
create_tables() (in module gpf.pheno.pheno_import)
create_test_study() (in module enrichment_api.tests.conftest)
CriteriaFilter (class in gpf.person_filters.person_filters)
criterias (gpf.gene_sets.denovo_gene_sets_config.DGSSpec attribute)
cshl_format() (in module gpf.variants.variant)
cshl_location (gpf.variants.variant.SummaryAllele property)
(gpf.variants.variant.SummaryVariant property)
cshl_position (gpf.variants.variant.SummaryAllele property)
cshl_variant (gpf.variants.variant.SummaryAllele property)
(gpf.variants.variant.SummaryVariant property)
cshl_variant_full (gpf.variants.variant.SummaryAllele property)
(gpf.variants.variant.SummaryVariant property)
current_idx (gpf.parquet.schema2.loader.MultiReader property)
(gpf.parquet.schema2.loader.Reader property)
curve_p0() (gpf.pedigrees.layout.Line method)
curve_p1() (gpf.pedigrees.layout.Line method)
curve_p2() (gpf.pedigrees.layout.Line method)
curve_p3() (gpf.pedigrees.layout.Line method)
curve_y_at() (gpf.pedigrees.layout.Line method)
curved (gpf.pedigrees.layout.Line property)
custom_query_transformer() (in module studies.conftest)
custom_response_transformer() (in module studies.conftest)
custom_wgpf() (in module datasets_api.tests.conftest)
(in module studies.conftest)
custom_wgpf_module() (in module datasets_api.tests.conftest)
(in module studies.conftest)
CustomFormatter (class in gpf_web.default_settings)
D
dad (gpf.variants.attributes.Role attribute)
dae (gpf.testing.import_helpers.StudyInputLayout attribute)
dae_import() (in module gpf.testing.import_helpers)
dae_liftover_main() (in module gpf.tools.liftover_tools)
dae_study() (in module gpf.testing.import_helpers)
DaeLiftoverTool (class in gpf.tools.liftover_tools)
DaeTransmittedFamiliesGenotypes (class in gpf.variants_loaders.dae.loader)
DaeTransmittedLoader (class in gpf.variants_loaders.dae.loader)
dangling() (gpf.pedigrees.pedigrees.Realization method)
dangling_set() (gpf.pedigrees.pedigrees.Realization method)
data_dictionary (gpf.pheno.common.PhenoImportConfig attribute)
data_reset() (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method)
DataDictionaryConfig (class in gpf.pheno.common)
dataset() (in module studies.tests.test_study_group_person_sets_queries)
(in module studies.tests.test_study_wrapper_person_sets)
(in module studies.tests.test_study_wrapper_unique_variants_query)
DatasetHelpers (class in gpf.tools.dataset_helpers)
datasets_api
module
datasets_api.migrations
module
datasets_api.migrations.0001_initial
module
datasets_api.migrations.0002_dataset_groups
module
datasets_api.migrations.0003_alter_dataset_options
module
datasets_api.migrations.0004_dataset_broken
module
datasets_api.migrations.0005_dataset_dataset_name
module
datasets_api.migrations.0006_datasethierarchy
module
datasets_api.migrations.0007_datasethierarchy_direct
module
datasets_api.migrations.0008_datasethierarchy_instance_id
module
datasets_api.tests
module
datasets_api.tests.conftest
module
db (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute)
(gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute)
Db2Layout (class in gpf.query_variants.sql.schema2.sql_query_builder)
db_name (gpf.pheno.pheno_import.MeasureReport attribute)
default (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute)
(gpf.person_sets.PersonSetCollectionConfig attribute)
DEFAULT_COMPRESSION (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter attribute)
(gpf.parquet.schema2.variants_parquet_writer.ContinuousParquetFileWriter attribute)
default_setters (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute)
DefaultBox (class in gpf.configuration.gpf_config_parser)
DefaultGenotypeStorage (class in gpf.gpf_instance.adjustments.gpf_instance_adjustments)
degree() (gpf.pedigrees.pedigrees.Realization method)
del_loader_prefix() (gpf.import_tools.import_tools.ImportProject static method)
DeleteAttributesFromVariantFilter (class in gpf.parquet.schema2.processing_pipeline)
DeleteAttributesFromVariantsBatchFilter (class in gpf.parquet.schema2.processing_pipeline)
delimiter (gpf.pheno.common.DataDictionaryConfig attribute)
(gpf.pheno.common.InstrumentConfig attribute)
(gpf.pheno.common.InstrumentDictionaryConfig attribute)
(gpf.pheno.common.PhenoImportConfig attribute)
(gpf.pheno.pheno_import.ImportInstrument attribute)
denovo (gpf.testing.import_helpers.StudyInputLayout attribute)
(gpf.variants.attributes.Inheritance attribute)
(gpf.variants.attributes.TransmissionType attribute)
denovo_1() (in module enrichment_api.tests.test_t4c8_enrichment)
denovo_gene_sets_db (gpf.gpf_instance.gpf_instance.GPFInstance property)
(gpf.gpf_instance.GPFInstance property)
denovo_gene_sets_types (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb property)
denovo_import() (in module gpf.testing.import_helpers)
denovo_liftover_main() (in module gpf.tools.liftover_tools)
denovo_study() (in module gpf.testing.import_helpers)
DenovoFamiliesGenotypes (class in gpf.variants_loaders.dae.loader)
DenovoGeneSetCollection (class in gpf.gene_sets.denovo_gene_set_collection)
DenovoGeneSetHelpers (class in gpf.gene_sets.denovo_gene_set_helpers)
DenovoGeneSetsConfig (class in gpf.gene_sets.denovo_gene_sets_config)
DenovoGeneSetsDb (class in gpf.gene_sets.denovo_gene_sets_db)
DenovoLiftoverTool (class in gpf.tools.liftover_tools)
DenovoLoader (class in gpf.variants_loaders.dae.loader)
DenovoReport (class in gpf.common_reports.denovo_report)
DenovoReportTable (class in gpf.common_reports.denovo_report)
dependencies (datasets_api.migrations.0001_initial.Migration attribute)
(datasets_api.migrations.0002_dataset_groups.Migration attribute)
(datasets_api.migrations.0003_alter_dataset_options.Migration attribute)
(datasets_api.migrations.0004_dataset_broken.Migration attribute)
(datasets_api.migrations.0005_dataset_dataset_name.Migration attribute)
(datasets_api.migrations.0006_datasethierarchy.Migration attribute)
(datasets_api.migrations.0007_datasethierarchy_direct.Migration attribute)
(datasets_api.migrations.0008_datasethierarchy_instance_id.Migration attribute)
(query_state_save.migrations.0001_initial.Migration attribute)
(query_state_save.migrations.0002_auto_20190205_0736.Migration attribute)
(query_state_save.migrations.0003_querystate_origin_querystate_timestamp.Migration attribute)
(user_queries.migrations.0001_initial.Migration attribute)
(users_api.migrations.0001_initial.Migration attribute)
(users_api.migrations.0002_auto_20190424_0751.Migration attribute)
(users_api.migrations.0003_authenticationlog.Migration attribute)
(users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more.Migration attribute)
(users_api.migrations.0005_gpuserstate.Migration attribute)
description (gpf.genomic_scores.scores.ScoreDesc attribute)
(gpf.studies.study.CommonStudyMixin property)
(studies.study_wrapper.WDAEAbstractStudy property)
(studies.study_wrapper.WDAEStudy property)
description_column (gpf.pheno.common.DataDictionaryConfig attribute)
(gpf.pheno.common.InstrumentDictionaryConfig attribute)
deselected_family_tags (gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute)
deserialize_family_record() (gpf.parquet.schema2.serializers.JsonVariantsDataSerializer method)
(gpf.parquet.schema2.serializers.VariantsDataSerializer method)
deserialize_family_variant() (gpf.query_variants.base_query_variants.QueryVariantsBase method)
deserialize_summary_record() (gpf.parquet.schema2.serializers.JsonVariantsDataSerializer method)
(gpf.parquet.schema2.serializers.VariantsDataSerializer method)
deserialize_summary_variant() (gpf.query_variants.base_query_variants.QueryVariantsBase method)
destination (gpf.pheno.common.PhenoImportConfig attribute)
DestinationConfig (class in gpf.pheno.common)
details (gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.variant.SummaryAllele property)
(gpf.variants.variant.SummaryVariant property)
determine_destination() (in module gpf.pheno.pheno_import)
determine_histogram_type() (in module gpf.pheno.prepare.measure_classifier)
DGSCQuery (class in gpf.gene_sets.denovo_gene_sets_config)
DGSSpec (class in gpf.gene_sets.denovo_gene_sets_config)
Dialect (class in gpf.query_variants.sql.schema2.base_query_builder)
dictionary (gpf.pheno.common.InstrumentDescriptionsConfig attribute)
(gpf.pheno.common.MeasureDescriptionsConfig attribute)
diff() (gpf.pedigrees.family.Person method)
disable_study_config() (gpf.tools.dataset_helpers.DatasetHelpers method)
display_name (gpf.pheno.common.RegressionMeasure attribute)
(gpf.variants.attributes.Role property)
DISPLAY_NAME_TYPE (gpf.variants.core.Allele attribute)
do_measure_build() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method)
do_study_config() (gpf.duckdb_storage.duckdb_import_storage.AbstractDuckDbImportStorage class method)
domain (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute)
(gpf.person_sets.PersonSetCollectionConfig attribute)
(gpf.pheno.pheno_data.Measure property)
domain_json() (gpf.person_sets.person_sets.PersonSetCollection method)
(gpf.person_sets.PersonSetCollection method)
download_sources() (in module genotype_browser.tests.conftest)
draw() (gpf.pedigrees.drawing.OffsetLayoutDrawer method)
draw_categorical_violin_distribution() (in module gpf.pheno.graphs)
draw_families() (in module gpf.tools.draw_pedigree)
draw_families_report() (in module gpf.tools.draw_pedigree)
draw_linregres() (in module gpf.pheno.graphs)
draw_measure_violinplot() (in module gpf.pheno.graphs)
draw_ordinal_violin_distribution() (in module gpf.pheno.graphs)
draw_pedigree() (in module gpf.tools.draw_pedigree)
drop_gp_table() (gpf.gene_profile.db.GeneProfileDBWriter method)
DuckDb2Runner (class in gpf.duckdb_storage.duckdb2_variants)
DuckDb2Variants (class in gpf.duckdb_storage.duckdb2_variants)
duckdb_connect() (in module gpf.duckdb_storage.duckdb_legacy_genotype_storage)
duckdb_parquet_storage_factory() (in module gpf.duckdb_storage.duckdb_genotype_storage)
duckdb_s3_parquet_storage_factory() (in module gpf.duckdb_storage.duckdb_genotype_storage)
duckdb_s3_storage_factory() (in module gpf.duckdb_storage.duckdb_genotype_storage)
duckdb_storage_factory() (in module gpf.duckdb_storage.duckdb_genotype_storage)
DuckDbBaseConf (class in gpf.duckdb_storage.duckdb_storage_config)
DuckDbConf (class in gpf.duckdb_storage.duckdb_storage_config)
DuckDbConnectionFactory (class in gpf.duckdb_storage.duckdb_connection_factory)
DuckDbImportStorage (class in gpf.duckdb_storage.duckdb_import_storage)
DuckDbLegacyImportStorage (class in gpf.duckdb_storage.duckdb_import_storage)
DuckDbLegacyStorage (class in gpf.duckdb_storage.duckdb_legacy_genotype_storage)
DuckDbParquetConf (class in gpf.duckdb_storage.duckdb_storage_config)
DuckDbParquetImportStorage (class in gpf.duckdb_storage.duckdb_import_storage)
DuckDbParquetStorage (class in gpf.duckdb_storage.duckdb_genotype_storage)
DuckDbQueryDialect (class in gpf.duckdb_storage.duckdb_variants)
DuckDbRunner (class in gpf.duckdb_storage.duckdb_variants)
DuckDbS3Conf (class in gpf.duckdb_storage.duckdb_storage_config)
DuckDbS3ImportStorage (class in gpf.duckdb_storage.duckdb_import_storage)
DuckDbS3ParquetConf (class in gpf.duckdb_storage.duckdb_storage_config)
DuckDbS3ParquetImportStorage (class in gpf.duckdb_storage.duckdb_import_storage)
DuckDbS3ParquetStorage (class in gpf.duckdb_storage.duckdb_genotype_storage)
DuckDbS3Storage (class in gpf.duckdb_storage.duckdb_genotype_storage)
DuckDbStorage (class in gpf.duckdb_storage.duckdb_genotype_storage)
DuckDbVariants (class in gpf.duckdb_storage.duckdb_variants)
E
effect (gpf.enrichment_tool.genotype_helper.GeneEffect attribute)
effect_gene_symbols (gpf.variants.variant.SummaryAllele property)
(gpf.variants.variant.SummaryVariant property)
effect_genes (gpf.enrichment_tool.genotype_helper.AlleleEvent attribute)
(gpf.variants.variant.SummaryAllele property)
effect_types (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute)
(gpf.variants.variant.SummaryAllele property)
(gpf.variants.variant.SummaryVariant property)
effect_types() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
EffectCell (class in gpf.common_reports.denovo_report)
EffectRow (class in gpf.common_reports.denovo_report)
effects (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute)
(gpf.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute)
(gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.variant.SummaryAllele property)
(gpf.variants.variant.SummaryVariant property)
EffectsCriteria (class in gpf.gene_sets.denovo_gene_sets_config)
enabled (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute)
EnableDisableStudies (class in gpf.gpf_instance.adjustments.gpf_instance_adjustments)
end (gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute)
end_position (gpf.variants.core.Allele property)
(gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
(gpf.variants.variant.SummaryVariant property)
endpoint_url (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute)
enforce_csrf() (utils.authentication.SessionAuthenticationWithoutCSRF method)
enrichment_api
module
enrichment_api.enrichment_builder
module
enrichment_api.enrichment_helper
module
enrichment_api.enrichment_serializer
module
enrichment_api.tests
module
enrichment_api.tests.conftest
module
enrichment_api.tests.test_enrichment_api
module
enrichment_api.tests.test_enrichment_builder
module
enrichment_api.tests.test_enrichment_helper_simple
module
enrichment_api.tests.test_enrichment_serializer
module
enrichment_api.tests.test_t4c8_enrichment
module
enrichment_builder() (in module enrichment_api.tests.conftest)
enrichment_cache_path (studies.study_wrapper.WDAEAbstractStudy property)
enrichment_config (studies.study_wrapper.WDAEAbstractStudy property)
enrichment_helper() (in module enrichment_api.tests.conftest)
enrichment_serializer() (in module enrichment_api.tests.conftest)
enrichment_test() (enrichment_api.enrichment_builder.BaseEnrichmentBuilder method)
(enrichment_api.enrichment_builder.EnrichmentBuilder method)
EnrichmentBackgroundResourceImplementation (class in gpf.enrichment_tool.resource_implementations.enrichment_resource_impl)
EnrichmentBuilder (class in enrichment_api.enrichment_builder)
EnrichmentHelper (class in enrichment_api.enrichment_helper)
EnrichmentResult (class in gpf.enrichment_tool.event_counters)
EnrichmentSerializer (class in enrichment_api.enrichment_serializer)
EnrichmentSingleResult (class in gpf.enrichment_tool.event_counters)
ERROR (gpf.tools.gpf_validation_runner.TestStatus attribute)
error_case_count (gpf.tools.gpf_validation_runner.AbstractRunner property)
errors_case_count (gpf.tools.gpf_validation_runner.MainRunner property)
escape_char() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method)
(gpf.query_variants.sql.schema2.base_query_builder.Dialect static method)
escape_quote_char() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method)
(gpf.query_variants.sql.schema2.base_query_builder.Dialect static method)
event_counts() (gpf.enrichment_tool.event_counters.CounterBase method)
EventCountersResult (class in gpf.enrichment_tool.event_counters)
events() (gpf.enrichment_tool.event_counters.CounterBase method)
(gpf.enrichment_tool.event_counters.EventsCounter method)
(gpf.enrichment_tool.event_counters.GeneEventsCounter method)
EventsCounter (class in gpf.enrichment_tool.event_counters)
EventsResult (class in gpf.enrichment_tool.event_counters)
execute() (gpf.gpf_instance.adjustments.adjust_command.AdjustmentsCommand method)
(gpf.gpf_instance.adjustments.adjust_duckdb_storage.AdjustDuckDbStorageCommand method)
(gpf.gpf_instance.adjustments.adjust_impala_storage.AdjustImpalaStorageCommand method)
(gpf.gpf_instance.adjustments.gpf_instance_adjustments.DefaultGenotypeStorage method)
(gpf.gpf_instance.adjustments.gpf_instance_adjustments.EnableDisableStudies method)
(gpf.gpf_instance.adjustments.gpf_instance_adjustments.InstanceIdCommand method)
expand_gene_set() (in module utils.expand_gene_set)
expand_gene_syms() (in module utils.expand_gene_set)
extend() (gpf.pedigrees.pedigrees.Realization method)
extract_person_set_collection_query() (studies.query_transformer.QueryTransformer method)
(studies.study_wrapper.QueryTransformerProtocol method)
F
F (gpf.variants.attributes.Sex attribute)
f1_trio() (in module enrichment_api.tests.conftest)
f1_trio_variants() (in module enrichment_api.tests.conftest)
FAIL (gpf.tools.gpf_validation_runner.TestStatus attribute)
failed_case_count (gpf.tools.gpf_validation_runner.AbstractRunner property)
(gpf.tools.gpf_validation_runner.MainRunner property)
families (gpf.pheno.pheno_data.PhenotypeData property)
(gpf.pheno.pheno_data.PhenotypeGroup property)
(gpf.pheno.pheno_data.PhenotypeStudy property)
(gpf.query_variants.base_query_variants.QueryVariants property)
(gpf.studies.study.GenotypeData property)
(gpf.studies.study.GenotypeDataGroup property)
(gpf.studies.study.GenotypeDataStudy property)
(studies.study_wrapper.WDAEAbstractStudy property)
families_of_persons() (gpf.pedigrees.families_data.FamiliesData method)
FamiliesData (class in gpf.pedigrees.families_data)
FamiliesGenotypes (class in gpf.variants_loaders.raw.loader)
FamiliesGroupCounters (class in gpf.common_reports.family_counter)
FamiliesLoader (class in gpf.pedigrees.loader)
FamiliesReport (class in gpf.common_reports.family_report)
Family (class in gpf.pedigrees.family)
family (gpf.common_reports.family_counter.FamilyCounter property)
(gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute)
(gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute)
family_allele_indexes (gpf.variants.family_variant.FamilyVariant property)
family_alleles (gpf.variants.family_variant.FamilyVariant property)
family_alt_alleles (gpf.variants.family_variant.FamilyVariant property)
family_api
module
family_api.tests
module
family_api.tests.test_family_api
module
family_attributes (gpf.variants.family_variant.FamilyAllele property)
family_base() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
family_best_state (gpf.variants.family_variant.FamilyVariant property)
family_bin (gpf.parquet.partition_descriptor.Partition attribute)
(gpf.pedigrees.family.Person property)
FAMILY_BIN_HEURISTIC_CUTOFF (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase attribute)
family_bins (gpf.query_variants.sql.schema2.sql_query_builder.QueryHeuristics attribute)
family_bins() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
FAMILY_COLUMNS (gpf.parquet.schema2.loader.ParquetLoader attribute)
family_genotype (gpf.variants.family_variant.FamilyVariant property)
family_genotype_iterator() (gpf.variants_loaders.dae.loader.DaeTransmittedFamiliesGenotypes method)
(gpf.variants_loaders.dae.loader.DenovoFamiliesGenotypes method)
(gpf.variants_loaders.raw.loader.FamiliesGenotypes method)
(gpf.variants_loaders.vcf.loader.VcfFamiliesGenotypes method)
family_id (gpf.enrichment_tool.genotype_helper.VariantEvent attribute)
(gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
family_ids() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
family_index (gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
family_partition() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
family_partition_schema() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
family_query() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method)
family_variant_filter_function() (gpf.inmemory_storage.raw_variants.RawFamilyVariants class method)
family_variants (gpf.variants_loaders.raw.loader.FullVariant attribute)
family_variants() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method)
family_variants_iterator() (gpf.inmemory_storage.raw_variants.RawFamilyVariants method)
(gpf.variants_loaders.raw.loader.VariantsLoader method)
FamilyAllele (class in gpf.variants.family_variant)
FamilyAlleleParquetSerializer (class in gpf.parquet.schema2.serializers)
FamilyConnections (class in gpf.pedigrees.pedigrees)
FamilyCounter (class in gpf.common_reports.family_counter)
FamilyFilter (class in gpf.person_filters)
(class in gpf.person_filters.person_filters)
FamilyQueryBuilder (class in gpf.query_variants.sql.schema2.family_builder)
FamilyRoleBuilder (class in gpf.pedigrees.family_role_builder)
FamilyTag (class in gpf.pedigrees.family)
FamilyTagsBuilder (class in gpf.pedigrees.family_tag_builder)
FamilyVariant (class in gpf.variants.family_variant)
favicon() (in module gpfjs.views)
female (gpf.enrichment_tool.event_counters.EnrichmentResult attribute)
(gpf.enrichment_tool.event_counters.EventCountersResult attribute)
(gpf.enrichment_tool.event_counters.EventsResult attribute)
(gpf.enrichment_tool.event_counters.VariantEventsResult attribute)
(gpf.person_sets.ChildrenBySex attribute)
(gpf.person_sets.ChildrenStats attribute)
(gpf.person_sets.person_sets.ChildrenBySex attribute)
(gpf.person_sets.person_sets.ChildrenStats attribute)
(gpf.variants.attributes.Sex attribute)
FEMALE_PRB (gpf.pedigrees.family.FamilyTag attribute)
females_count() (gpf.pheno.graphs.GraphColumn method)
fetch() (gpf.parquet.schema2.processing_pipeline.Schema2SummaryVariantsBatchSource method)
(gpf.parquet.schema2.processing_pipeline.Schema2SummaryVariantsSource method)
(gpf.parquet.schema2.processing_pipeline.VariantsLoaderBatchSource method)
(gpf.parquet.schema2.processing_pipeline.VariantsLoaderSource method)
(gpf.variants_loaders.raw.loader.VariantsLoader method)
fetch_annotation() (gpf.duckdb_storage.duckdb2_variants.DuckDb2Variants method)
fetch_family_variants() (gpf.parquet.schema2.loader.ParquetLoader method)
(gpf.variants_loaders.raw.loader.VariantsLoader method)
fetch_summary_variants() (gpf.parquet.schema2.loader.ParquetLoader method)
(gpf.variants_loaders.raw.loader.VariantsLoader method)
fetch_variants() (gpf.parquet.schema2.loader.ParquetLoader method)
fgt2str() (in module gpf.utils.variant_utils)
figure_filepath() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method)
filename (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentResourceBackground property)
(gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property)
files (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation property)
(gpf.pheno.common.InstrumentDescriptionsConfig attribute)
(gpf.pheno.common.MeasureDescriptionsConfig attribute)
(gpf.pheno.pheno_import.ImportInstrument attribute)
filetype_parsers (gpf.configuration.gpf_config_parser.GPFConfigParser attribute)
fill_family_bins() (in module gpf.parquet.parquet_writer)
filter() (gpf.parquet.schema2.processing_pipeline.AnnotationPipelineVariantsBatchFilter method)
(gpf.parquet.schema2.processing_pipeline.AnnotationPipelineVariantsFilter method)
(gpf.parquet.schema2.processing_pipeline.DeleteAttributesFromVariantFilter method)
(gpf.parquet.schema2.processing_pipeline.DeleteAttributesFromVariantsBatchFilter method)
(gpf.parquet.schema2.variants_parquet_writer.Schema2SummaryVariantBatchConsumer method)
(gpf.parquet.schema2.variants_parquet_writer.Schema2SummaryVariantConsumer method)
(gpf.parquet.schema2.variants_parquet_writer.Schema2VariantBatchConsumer method)
(gpf.parquet.schema2.variants_parquet_writer.Schema2VariantConsumer method)
filter_allele() (gpf.inmemory_storage.raw_variants.RawFamilyVariants class method)
filter_denovo_one_event_per_family() (in module gpf.enrichment_tool.event_counters)
filter_denovo_one_gene_per_events() (in module gpf.enrichment_tool.event_counters)
filter_denovo_one_gene_per_recurrent_events() (in module gpf.enrichment_tool.event_counters)
filter_family_variant() (gpf.inmemory_storage.raw_variants.RawFamilyVariants class method)
filter_gene_effects() (gpf.inmemory_storage.raw_variants.RawFamilyVariants static method)
filter_overlapping_events() (in module gpf.enrichment_tool.event_counters)
filter_real_attr() (gpf.inmemory_storage.raw_variants.RawFamilyVariants static method)
filter_regions() (gpf.inmemory_storage.raw_variants.RawFamilyVariants static method)
FILTER_RENAMES_MAP (studies.query_transformer.QueryTransformer attribute)
filter_summary_allele() (gpf.inmemory_storage.raw_variants.RawFamilyVariants class method)
filter_summary_variant() (gpf.inmemory_storage.raw_variants.RawFamilyVariants class method)
find_dataset_id_in_dict() (in module utils.datasets)
find_dataset_id_in_request() (in module utils.datasets)
find_genotype_data_config() (gpf.tools.dataset_helpers.DatasetHelpers method)
find_genotype_data_config_file() (gpf.tools.dataset_helpers.DatasetHelpers method)
find_instrument_values_tables() (gpf.pheno.db.PhenoDb method)
find_storage() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method)
flexible_cnv_loader() (in module gpf.variants_loaders.cnv.flexible_cnv_loader)
flexible_denovo_load() (gpf.variants_loaders.dae.loader.DenovoLoader method)
flexible_pedigree_read() (gpf.pedigrees.loader.FamiliesLoader static method)
flexible_variant_loader() (in module gpf.variants_loaders.raw.flexible_variant_loader)
float_type() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method)
(gpf.query_variants.sql.schema2.base_query_builder.Dialect static method)
fmt_invert (gpf_web.default_settings.CustomFormatter attribute)
fmt_normal (gpf_web.default_settings.CustomFormatter attribute)
foobar_gpf() (in module gpf.testing.foobar_import)
force_extend() (gpf.pedigrees.pedigrees.Realization method)
force_type_inference() (in module gpf.pheno.prepare.measure_classifier)
format() (gpf_web.default_settings.CustomFormatter method)
FORMATS (gpf_web.default_settings.CustomFormatter attribute)
frequencies (gpf.variants.variant.SummaryVariant property)
frequency (gpf.variants.variant.SummaryAllele property)
frequency() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
frequency_bin (gpf.parquet.partition_descriptor.Partition attribute)
frequency_bins (gpf.query_variants.sql.schema2.sql_query_builder.QueryHeuristics attribute)
frequency_bins() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
from_ (gpf.person_sets.person_sets.SourceConfig attribute)
(gpf.person_sets.SourceConfig attribute)
from_cnv() (gpf.variants.variant.VariantDetails static method)
from_config() (gpf.pheno.storage.PhenotypeStorage static method)
from_dict() (gpf.configuration.study_config_builder.TOMLDict static method)
from_events_result() (gpf.enrichment_tool.event_counters.EventCountersResult static method)
from_families() (gpf.common_reports.family_counter.FamiliesGroupCounters static method)
(gpf.pedigrees.families_data.FamiliesData static method)
(gpf.person_sets.person_sets.PersonSetCollection static method)
(gpf.person_sets.PersonSetCollection static method)
from_families_data() (gpf.common_reports.family_report.FamiliesReport static method)
from_family() (gpf.common_reports.family_counter.FamilyCounter static method)
(gpf.pedigrees.layout.Layout static method)
(gpf.pedigrees.pedigrees.FamilyConnections class method)
from_family_layout() (gpf.pedigrees.layout.Layout static method)
from_family_persons() (gpf.pedigrees.families_data.FamiliesData static method)
from_genotype_study() (gpf.common_reports.denovo_report.DenovoReport static method)
from_json() (gpf.genomic_scores.scores.ScoreDesc static method)
(gpf.person_sets.person_sets.PersonSet static method)
(gpf.person_sets.PersonSet static method)
(gpf.pheno.pheno_data.Measure class method)
from_label() (gpf.pedigrees.family.FamilyTag static method)
from_list() (gpf.configuration.study_config_builder.TOMLList static method)
from_name() (gpf.variants.attributes.Inheritance static method)
(gpf.variants.attributes.Role static method)
(gpf.variants.attributes.Sex static method)
(gpf.variants.attributes.Status static method)
(gpf.variants.attributes.Zygosity static method)
from_pedigree_df() (gpf.pedigrees.families_data.FamiliesData static method)
from_person_set() (gpf.common_reports.people_counter.PeopleCounter static method)
from_person_set_collection() (gpf.common_reports.people_counter.PeopleCounters static method)
from_person_set_collections() (gpf.common_reports.people_counter.PeopleReport static method)
from_persons() (gpf.pedigrees.family.Family static method)
from_pylist() (gpf.parquet.partition_descriptor.Partition static method)
from_record() (gpf.pheno.pheno_data.Measure class method)
from_records() (gpf.pedigrees.family.Family static method)
from_row() (gpf.pheno.common.ImportManifest static method)
from_sets() (gpf.pedigrees.pedigrees.SandwichInstance static method)
from_str() (gpf.pheno.common.MeasureType static method)
from_study() (gpf.common_reports.family_report.FamiliesReport static method)
from_table() (gpf.pheno.common.ImportManifest static method)
from_value() (gpf.variants.attributes.Inheritance static method)
(gpf.variants.attributes.Role static method)
(gpf.variants.attributes.Sex static method)
(gpf.variants.attributes.Status static method)
(gpf.variants.attributes.Zygosity static method)
from_variants() (gpf.common_reports.denovo_report.DenovoReportTable static method)
from_vcf() (gpf.variants.variant.VariantDetails static method)
FrozenBox (class in gpf.configuration.gpf_config_parser)
full_members (gpf.pedigrees.family.Family property)
full_variants (gpf.inmemory_storage.raw_variants.RawMemoryVariants property)
full_variants_iterator() (gpf.inmemory_storage.raw_variants.RawFamilyVariants method)
(gpf.inmemory_storage.raw_variants.RawMemoryVariants method)
(gpf.variants_loaders.cnv.loader.CNVLoader method)
(gpf.variants_loaders.dae.loader.DenovoLoader method)
(gpf.variants_loaders.raw.loader.VariantsGenotypesLoader method)
(gpf.variants_loaders.raw.loader.VariantsLoader method)
FullVariant (class in gpf.variants_loaders.raw.loader)
fv1() (in module studies.tests.test_response_transformer_columns)
fv2() (in module studies.tests.test_response_transformer_columns)
fvuid (gpf.enrichment_tool.genotype_helper.VariantEvent attribute)
(gpf.variants.family_variant.FamilyVariant property)
G
GAP (gpf.pedigrees.drawing.OffsetLayoutDrawer attribute)
gender_palette() (in module gpf.pheno.graphs)
gender_palette_light() (in module gpf.pheno.graphs)
gene (gpf.enrichment_tool.genotype_helper.GeneEffect attribute)
gene_models (gpf.gpf_instance.gpf_instance.GPFInstance property)
(gpf.gpf_instance.GPFInstance property)
gene_profiles_api
module
gene_profiles_api.tests
module
gene_profiles_api.tests.test_agp_api
module
gene_profiles_api.tests.test_agp_api_configless
module
GENE_REGIONS_HEURISTIC_CUTOFF (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute)
(gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase attribute)
GENE_REGIONS_HEURISTIC_EXTEND (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute)
(gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase attribute)
gene_scores
module
gene_scores.tests
module
gene_scores.tests.conftest
module
gene_scores.tests.test_gene_scores
module
gene_scores.tests.test_gene_scores_db
module
gene_scores.tests.test_gene_scores_views
module
gene_scores.tests.test_scores_partitions
module
gene_scores_db (gpf.gpf_instance.gpf_instance.GPFInstance property)
(gpf.gpf_instance.GPFInstance property)
gene_scores_db() (in module gene_scores.tests.conftest)
gene_set_id (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute)
(gpf.gene_sets.denovo_gene_sets_config.DGSSpec attribute)
gene_sets
module
gene_sets.tests
module
gene_sets.tests.test_gene_sets_api
module
gene_sets_db (gpf.gpf_instance.gpf_instance.GPFInstance property)
(gpf.gpf_instance.GPFInstance property)
gene_sets_ids (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute)
gene_view
module
gene_view.tests
module
gene_view.tests.test_gene_view
module
GeneEffect (class in gpf.enrichment_tool.genotype_helper)
GeneEventsCounter (class in gpf.enrichment_tool.event_counters)
GeneProfileDB (class in gpf.gene_profile.db)
GeneProfileDBWriter (class in gpf.gene_profile.db)
generate_gp() (in module gpf.gene_profile.generate_gene_profile)
generate_import_manifests() (gpf.pheno.pheno_data.PhenotypeData method)
(gpf.pheno.pheno_data.PhenotypeGroup method)
(gpf.pheno.pheno_data.PhenotypeStudy method)
generate_import_task_graph() (gpf.duckdb_storage.duckdb_import_storage.AbstractDuckDbImportStorage method)
(gpf.import_tools.import_tools.ImportStorage method)
(gpf.inmemory_storage.inmemory_import_storage.InmemoryImportStorage method)
(gpf.parquet_storage.storage.ParquetImportStorage method)
(gpf.schema2_storage.schema2_import_storage.Schema2ImportStorage method)
generate_instrument_table_name() (in module gpf.pheno.db)
generate_phenotype_data_config() (in module gpf.pheno.pheno_import)
generate_reannotate_task_graph() (gpf.schema2_storage.schema2_import_storage.Schema2ImportStorage static method)
generated (gpf.pedigrees.family.Person property)
generation_ranks() (gpf.pedigrees.pedigrees.IndividualGroup method)
genes() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
genes_prob() (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method)
(gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method)
genes_weight() (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method)
(gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method)
GeneScoreEnrichmentBackground (class in gpf.enrichment_tool.gene_weights_background)
GeneSetsDb (class in gpf.gene_sets.gene_sets_db)
genetic_model (gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
GeneticModel (class in gpf.variants.attributes)
GeneWeightsEnrichmentBackground (class in gpf.enrichment_tool.gene_weights_background)
genomes_api
module
genomes_api.tests
module
genomes_api.tests.test_gene_models_api
module
genomic_scores (gpf.gpf_instance.gpf_instance.GPFInstance property)
(gpf.gpf_instance.GPFInstance property)
genomic_scores_api
module
genomic_scores_api.tests
module
genomic_scores_api.tests.test_genomic_scores_api
module
GenomicScoresRegistry (class in gpf.genomic_scores.scores)
genotype (gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
genotype_browser
module
genotype_browser.tests
module
genotype_browser.tests.conftest
module
genotype_browser.tests.test_effect_types_download
module
genotype_browser.tests.test_pheno_columns
module
genotype_browser.tests.test_pheno_filters
module
genotype_data (studies.study_wrapper.WDAEAbstractStudy property)
genotype_data_persons() (gpf.pheno_tool.tool.PhenoToolHelper method)
genotype_data_variants() (gpf.pheno_tool.tool.PhenoToolHelper method)
genotype_storages (gpf.gpf_instance.gpf_instance.GPFInstance property)
(gpf.gpf_instance.GPFInstance property)
GenotypeBrowserRunner (class in gpf.tools.gpf_validation_runner)
GenotypeData (class in gpf.studies.study)
GenotypeDataGroup (class in gpf.studies.study)
GenotypeDataStudy (class in gpf.studies.study)
GenotypeHelper (class in gpf.enrichment_tool.genotype_helper)
GenotypeStorage (class in gpf.genotype_storage.genotype_storage)
GenotypeStorageRegistry (class in gpf.genotype_storage.genotype_storage_registry)
get() (gpf.pedigrees.families_data.FamiliesData method)
(gpf.studies.variants_db.VariantsDb method)
get_active_vertex_edges() (gpf.pedigrees.pedigrees.Realization method)
get_active_vertices() (gpf.pedigrees.pedigrees.Realization method)
get_all_gene_score_descs() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
get_all_gene_scores() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
get_all_gene_sets() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection class method)
(gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method)
(gpf.gene_sets.gene_sets_db.GeneSetsDb method)
get_all_genotype_data() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
(gpf.studies.variants_db.VariantsDb method)
get_all_genotype_group_ids() (gpf.studies.variants_db.VariantsDb method)
get_all_genotype_groups() (gpf.studies.variants_db.VariantsDb method)
get_all_genotype_storage_ids() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method)
get_all_genotype_storages() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method)
get_all_genotype_studies() (gpf.studies.variants_db.VariantsDb method)
get_all_genotype_study_ids() (gpf.studies.variants_db.VariantsDb method)
get_all_phenotype_data() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
(gpf.pheno.registry.PhenoRegistry method)
get_all_phenotype_storage_ids() (gpf.pheno.storage.PhenotypeStorageRegistry method)
get_all_phenotype_storages() (gpf.pheno.storage.PhenotypeStorageRegistry method)
get_annotatable() (gpf.variants.core.Allele method)
get_annotation_pipeline() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
get_annotation_pipeline_config() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
(gpf.import_tools.import_tools.ImportProject method)
get_argument_parser() (gpf.tools.reannotate_instance.ReannotateInstanceTool method)
get_attr() (gpf.pedigrees.family.Person method)
get_attribute() (gpf.variants.family_variant.FamilyAllele method)
(gpf.variants.variant.SummaryAllele method)
(gpf.variants.variant.SummaryVariant method)
(gpf.variants_loaders.raw.loader.VariantsLoader method)
(gpf.variants_loaders.raw.loader.VariantsLoaderDecorator method)
get_base_dir() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method)
get_bbox() (gpf.pedigrees.layout.Layout method)
get_cache_path() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
get_children() (gpf.person_sets.person_sets.PersonSet method)
(gpf.person_sets.PersonSet method)
get_children_by_sex() (gpf.person_sets.person_sets.PersonSet method)
(gpf.person_sets.PersonSet method)
get_children_count() (gpf.person_sets.person_sets.PersonSet method)
(gpf.person_sets.PersonSet method)
get_children_ids() (gpf.pheno.pheno_data.PhenotypeData method)
(gpf.pheno.pheno_data.PhenotypeGroup method)
(gpf.pheno.pheno_data.PhenotypeStudy method)
(gpf.studies.study.GenotypeData method)
(gpf.studies.study.GenotypeDataGroup method)
(gpf.studies.study.GenotypeDataStudy method)
(studies.study_wrapper.WDAEAbstractStudy method)
(studies.study_wrapper.WDAEStudyGroup method)
get_children_stats() (gpf.person_sets.person_sets.PersonSet method)
(gpf.person_sets.PersonSet method)
get_clean_config() (in module studies.study_wrapper)
get_collection_types_legend() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method)
get_column_sources() (studies.study_wrapper.WDAEStudy method)
get_columns() (gpf.pedigrees.family.Family method)
get_columns_as_sources() (studies.study_wrapper.WDAEStudy static method)
get_columns_to_draw() (in module gpf.pheno.graphs)
get_common_report() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method)
(common_reports_api.common_reports_helper.CommonReportsHelper method)
(gpf.pheno.pheno_data.PhenotypeData method)
(gpf.studies.study.GenotypeData method)
get_context_genotype_storages() (in module gpf.genotype_storage.genotype_storage_genomic_context_cli)
get_context_keys() (gpf.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceGenomicContext method)
get_context_object() (gpf.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceGenomicContext method)
get_count() (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method)
(pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method)
get_data_dir() (gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method)
get_dataset() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
get_db() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method)
get_db_filename() (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage method)
(gpf.duckdb_storage.duckdb_genotype_storage.DuckDbStorage method)
(gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method)
get_default_background_model() (enrichment_api.enrichment_helper.EnrichmentHelper method)
get_default_counting_model() (enrichment_api.enrichment_helper.EnrichmentHelper method)
get_default_genotype_storage() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method)
get_default_phenotype_storage() (gpf.pheno.storage.PhenotypeStorageRegistry method)
get_denovo_events() (gpf.enrichment_tool.genotype_helper.GenotypeHelper method)
get_denovo_gene_set_spec() (in module utils.gene_sets)
get_empty() (gpf.common_reports.denovo_report.EffectRow method)
get_enrichment_cache_path() (in module gpf.enrichment_tool.enrichment_utils)
get_enrichment_config() (in module gpf.enrichment_tool.enrichment_utils)
get_enrichment_models() (enrichment_api.enrichment_helper.BaseEnrichmentHelper method)
(enrichment_api.enrichment_helper.EnrichmentHelper method)
get_family_counter_list() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method)
(common_reports_api.common_reports_helper.CommonReportsHelper method)
get_family_counter_tsv() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method)
(common_reports_api.common_reports_helper.CommonReportsHelper method)
get_family_data_tsv() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method)
(common_reports_api.common_reports_helper.CommonReportsHelper method)
get_family_pedigree() (in module gpf.common_reports.family_counter)
get_family_pq_filepaths() (gpf.parquet.schema2.loader.ParquetLoader method)
get_family_read_counts() (gpf.variants_loaders.dae.loader.DaeTransmittedFamiliesGenotypes method)
get_family_type() (in module gpf.common_reports.family_counter)
get_filtered_family_data_tsv() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method)
(common_reports_api.common_reports_helper.CommonReportsHelper method)
get_full_common_report() (common_reports_api.common_reports_helper.BaseCommonReportsHelper method)
(common_reports_api.common_reports_helper.CommonReportsHelper method)
get_gene_score() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
get_gene_score_desc() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
get_gene_set() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method)
(gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method)
(gpf.gene_sets.gene_sets_db.GeneSetsDb method)
get_gene_set_collection_ids() (gpf.gene_sets.gene_sets_db.GeneSetsDb method)
get_gene_set_from_collections() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection class method)
get_gene_set_ids() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method)
(gpf.gene_sets.gene_sets_db.GeneSetsDb method)
get_gene_sets_types_legend() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method)
get_gene_view_summary_variants() (studies.study_wrapper.WDAEAbstractStudy method)
(studies.study_wrapper.WDAEStudy method)
get_gene_view_summary_variants_download() (studies.study_wrapper.WDAEAbstractStudy method)
(studies.study_wrapper.WDAEStudy method)
get_genotype_data() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
get_genotype_data_config() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
get_genotype_data_ids() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method)
(gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
get_genotype_group() (gpf.studies.variants_db.VariantsDb method)
get_genotype_group_config() (gpf.studies.variants_db.VariantsDb method)
get_genotype_storage() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method)
(gpf.import_tools.import_tools.ImportProject method)
(gpf.tools.dataset_helpers.DatasetHelpers method)
get_genotype_storage_factory() (in module gpf.genotype_storage.genotype_storage_registry)
get_genotype_storage_types() (in module gpf.genotype_storage.genotype_storage_registry)
get_genotype_study() (gpf.studies.variants_db.VariantsDb method)
get_genotype_study_config() (gpf.studies.variants_db.VariantsDb method)
get_gp() (gpf.gene_profile.db.GeneProfileDB method)
get_gp_configuration() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
get_gp_statistic() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
get_gpf_instance() (gpf.import_tools.import_tools.ImportProject method)
(in module gpf.pheno.pheno_import)
get_graph() (gpf.pedigrees.pedigrees.FamilyConnections method)
get_image() (gpf.pheno.pheno_data.PhenotypeData method)
(pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method)
(pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method)
get_import_storage() (gpf.import_tools.import_tools.ImportProject method)
get_import_storage_factory() (in module gpf.import_tools.import_tools)
get_import_storage_types() (in module gpf.import_tools.import_tools)
get_import_variants_buckets() (gpf.import_tools.import_tools.ImportProject method)
get_individual() (gpf.pedigrees.pedigrees.FamilyConnections method)
get_individuals() (gpf.pedigrees.pedigrees.FamilyConnections method)
get_individuals_with_rank() (gpf.pedigrees.pedigrees.FamilyConnections method)
get_info() (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method)
get_input_filenames() (gpf.import_tools.import_tools.ImportProject method)
get_instrument_measures() (gpf.pheno.pheno_data.PhenotypeData method)
get_instruments() (gpf.pheno.pheno_data.PhenotypeData method)
(pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method)
(pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method)
get_interval() (gpf.pedigrees.pedigrees.Realization method)
get_interval_locus_ploidy() (in module gpf.utils.variant_utils)
get_leaf_children() (gpf.studies.study.GenotypeData method)
get_leaves() (gpf.pheno.pheno_data.PhenotypeGroup method)
get_locus_ploidy() (in module gpf.utils.variant_utils)
get_mating_units() (gpf.pedigrees.pedigrees.FamilyConnections method)
get_maximal_set() (gpf.pedigrees.pedigrees.Realization method)
get_measure() (gpf.pheno.pheno_data.PhenotypeData method)
get_measure_description() (gpf.pheno.pheno_data.PhenotypeData method)
(pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method)
(pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method)
get_measure_ids() (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method)
(pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method)
get_measures() (gpf.pheno.pheno_data.PhenotypeData method)
(studies.study_wrapper.WDAEAbstractStudy method)
get_measures_df() (gpf.pheno.db.PhenoDb method)
get_measures_info() (gpf.pheno.pheno_data.PhenotypeData method)
(gpf.pheno.pheno_data.PhenotypeGroup method)
(gpf.pheno.pheno_data.PhenotypeStudy method)
(pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method)
(pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method)
get_measures_json() (studies.study_wrapper.WDAEAbstractStudy method)
(studies.study_wrapper.WDAEStudy method)
get_member() (gpf.pedigrees.family.Family method)
get_members_with_roles() (gpf.pedigrees.family.Family method)
get_members_with_statuses() (gpf.pedigrees.family.Family method)
get_memory_limit() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method)
get_normalize_measure_id() (gpf.pheno_tool.tool.PhenoTool method)
get_or_create_query_transformer() (in module studies.query_transformer)
get_or_create_response_transformer() (in module studies.response_transformer)
get_output_parquet_files_dir() (in module gpf.pheno.pheno_import)
get_paginated_response() (utils.pagination.WdaePageNumberPagination method)
get_parquet_dataset_dir() (gpf.import_tools.import_tools.ImportProject method)
get_partition_descriptor() (gpf.import_tools.import_tools.ImportProject method)
get_pedigree() (gpf.import_tools.import_tools.ImportProject method)
get_pedigree_column_names() (in module gpf.pedigrees.family)
get_pedigree_df() (gpf.pheno.db.PhenoDb method)
(gpf.pheno.pheno_data.PhenotypeData method)
(gpf.pheno.pheno_data.PhenotypeGroup method)
(gpf.pheno.pheno_data.PhenotypeStudy method)
get_pedigree_filename() (gpf.import_tools.import_tools.ImportProject method)
get_pedigree_loader() (gpf.import_tools.import_tools.ImportProject method)
get_pedigree_params() (gpf.import_tools.import_tools.ImportProject method)
get_people_measure_values() (gpf.pheno.db.PhenoDb method)
(gpf.pheno.pheno_data.PhenotypeData method)
(gpf.pheno.pheno_data.PhenotypeGroup method)
(gpf.pheno.pheno_data.PhenotypeStudy method)
get_people_measure_values_df() (gpf.pheno.db.PhenoDb method)
(gpf.pheno.pheno_data.PhenotypeData method)
(gpf.pheno.pheno_data.PhenotypeGroup method)
(gpf.pheno.pheno_data.PhenotypeStudy method)
get_person_color() (gpf.person_sets.person_sets.PersonSetCollection static method)
(gpf.person_sets.PersonSetCollection static method)
get_person_roles() (gpf.pheno.pheno_data.PhenotypeData method)
(gpf.pheno.pheno_data.PhenotypeGroup method)
get_person_set() (gpf.person_sets.person_sets.PersonSetCollection method)
(gpf.person_sets.PersonSetCollection method)
get_person_set_collection() (gpf.pheno.pheno_data.PhenotypeData method)
(gpf.studies.study.GenotypeData method)
(studies.study_wrapper.WDAEAbstractStudy method)
get_person_set_collection_legend() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method)
get_person_set_of_person() (gpf.person_sets.person_sets.PersonSetCollection method)
(gpf.person_sets.PersonSetCollection method)
get_persons() (gpf.pheno.pheno_data.PhenotypeData method)
get_persons_df() (gpf.pheno.db.PhenoDb method)
(gpf.pheno.pheno_data.PhenotypeData method)
(gpf.pheno.pheno_data.PhenotypeGroup method)
(gpf.pheno.pheno_data.PhenotypeStudy method)
get_pheno_browser_images_dir() (in module gpf.pheno.pheno_data)
get_pheno_cache_path() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
get_pheno_db_dir() (in module gpf.pheno.pheno_data)
get_phenotype_data() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
(gpf.pheno.registry.PhenoRegistry method)
get_phenotype_data_config() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
(gpf.pheno.registry.PhenoRegistry method)
get_phenotype_data_ids() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
(gpf.pheno.registry.PhenoRegistry method)
get_phenotype_storage() (gpf.pheno.storage.PhenotypeStorageRegistry method)
get_processing_annotation_batch_size() (gpf.import_tools.import_tools.ImportProject method)
get_processing_parquet_dataset_dir() (gpf.import_tools.import_tools.ImportProject method)
get_query_leaf_studies() (gpf.studies.study.GenotypeData method)
get_query_person_set_ids() (gpf.person_sets.person_sets.PersonSetCollection method)
(gpf.person_sets.PersonSetCollection method)
get_regression_measures() (gpf.pheno.prepare_data.PreparePhenoBrowserBase method)
get_regressions() (gpf.pheno.pheno_data.PhenotypeData method)
(gpf.pheno.pheno_data.PhenotypeGroup method)
(gpf.pheno.pheno_data.PhenotypeStudy method)
get_result_by_sex() (gpf.pheno_tool.pheno_tool_adapter.PhenoToolAdapter method)
(pheno_tool_api.adapter.PhenoToolAdapter method)
get_row_group_size() (gpf.import_tools.import_tools.ImportProject method)
get_schema() (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentResourceBackground static method)
(gpf.enrichment_tool.samocha_background.SamochaEnrichmentBackground static method)
get_scores() (gpf.genomic_scores.scores.GenomicScoresRegistry method)
get_selected_counting_models() (enrichment_api.enrichment_helper.EnrichmentHelper method)
get_selected_person_set_collections() (enrichment_api.enrichment_helper.EnrichmentHelper method)
get_sibship_units() (gpf.pedigrees.pedigrees.FamilyConnections method)
get_source() (gpf.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceGenomicContext method)
get_statistics_info() (gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation method)
get_stats() (gpf.person_sets.person_sets.PersonSetCollection method)
(gpf.person_sets.PersonSetCollection method)
get_storage_types() (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbParquetStorage class method)
(gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3ParquetStorage class method)
(gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage class method)
(gpf.duckdb_storage.duckdb_genotype_storage.DuckDbStorage class method)
(gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage class method)
(gpf.genotype_storage.genotype_storage.GenotypeStorage class method)
(gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage class method)
(gpf.parquet_storage.storage.ParquetGenotypeStorage class method)
get_studies() (gpf_instance.extension.GPFExtensionBase method)
get_studies_ids() (gpf.studies.study.GenotypeData method)
(gpf.studies.study.GenotypeDataGroup method)
(gpf.studies.study.GenotypeDataStudy method)
(gpf_instance.extension.GPFExtensionBase method)
(studies.study_wrapper.WDAEAbstractStudy method)
(studies.study_wrapper.WDAEStudyGroup method)
get_study_config_tables() (in module gpf.duckdb_storage.duckdb_storage_helpers)
get_summary_pq_filepaths() (gpf.parquet.schema2.loader.ParquetLoader method)
get_sym_2_fn() (in module gpf.enrichment_tool.event_counters)
get_tool() (gpf_instance.extension.GPFExtensionBase method)
get_transcript_models() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
get_unique_family_variants() (studies.query_transformer.QueryTransformer method)
(studies.study_wrapper.QueryTransformerProtocol method)
get_variant_loader() (gpf.import_tools.import_tools.ImportProject method)
get_variant_loader_chrom_lens() (gpf.import_tools.import_tools.ImportProject method)
get_variant_loader_chromosomes() (gpf.import_tools.import_tools.ImportProject method)
get_variant_loader_types() (gpf.import_tools.import_tools.ImportProject method)
get_variant_params() (gpf.import_tools.import_tools.ImportProject method)
get_variant_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
get_wgpf_instance() (in module gpf_instance.gpf_instance)
get_work_dir() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method)
gp_from_table_row() (gpf.gene_profile.db.GeneProfileDB method)
gp_from_table_row_single_view() (gpf.gene_profile.db.GeneProfileDB method)
gpf
module
gpf.common_reports
module
gpf.common_reports.common_report
module
gpf.common_reports.denovo_report
module
gpf.common_reports.family_counter
module
gpf.common_reports.family_report
module
gpf.common_reports.people_counter
module
gpf.configuration
module
gpf.configuration.gpf_config_parser
module
gpf.configuration.schemas
module
gpf.configuration.schemas.dae_conf
module
gpf.configuration.schemas.gene_profile
module
gpf.configuration.schemas.gene_weights_db
module
gpf.configuration.schemas.person_sets
module
gpf.configuration.schemas.phenotype_data
module
gpf.configuration.schemas.study_config
module
gpf.configuration.schemas.wdae_study_config
module
gpf.configuration.study_config_builder
module
gpf.configuration.utils
module
gpf.duckdb_storage
module
gpf.duckdb_storage.duckdb2_variants
module
gpf.duckdb_storage.duckdb_connection_factory
module
gpf.duckdb_storage.duckdb_genotype_storage
module
gpf.duckdb_storage.duckdb_import_storage
module
gpf.duckdb_storage.duckdb_legacy_genotype_storage
module
gpf.duckdb_storage.duckdb_storage_config
module
gpf.duckdb_storage.duckdb_storage_helpers
module
gpf.duckdb_storage.duckdb_variants
module
gpf.enrichment_tool
module
gpf.enrichment_tool.base_enrichment_background
module
gpf.enrichment_tool.build_coding_length_enrichment_background
module
gpf.enrichment_tool.build_ur_synonymous_enrichment_background
module
gpf.enrichment_tool.enrichment_cache_builder
module
gpf.enrichment_tool.enrichment_utils
module
gpf.enrichment_tool.event_counters
module
gpf.enrichment_tool.gene_weights_background
module
gpf.enrichment_tool.genotype_helper
module
gpf.enrichment_tool.resource_implementations
module
gpf.enrichment_tool.resource_implementations.enrichment_resource_impl
module
gpf.enrichment_tool.samocha_background
module
gpf.gene_profile
module
gpf.gene_profile.convert_gene_profile_to_duckdb
module
gpf.gene_profile.db
module
gpf.gene_profile.exporter
module
gpf.gene_profile.generate_gene_profile
module
gpf.gene_profile.statistic
module
gpf.gene_sets
module
gpf.gene_sets.denovo_gene_set_collection
module
gpf.gene_sets.denovo_gene_set_helpers
module
gpf.gene_sets.denovo_gene_sets_config
module
gpf.gene_sets.denovo_gene_sets_db
module
gpf.gene_sets.gene_sets_db
module
gpf.genomic_scores
module
gpf.genomic_scores.scores
module
gpf.genotype_storage
module
gpf.genotype_storage.genotype_storage
module
gpf.genotype_storage.genotype_storage_genomic_context_cli
module
gpf.genotype_storage.genotype_storage_registry
module
gpf.gpf_instance
module
gpf.gpf_instance.adjustments
module
gpf.gpf_instance.adjustments.adjust_command
module
gpf.gpf_instance.adjustments.adjust_duckdb_storage
module
gpf.gpf_instance.adjustments.adjust_impala_storage
module
gpf.gpf_instance.adjustments.gpf_instance_adjustments
module
gpf.gpf_instance.gpf_instance
module
gpf.gpf_instance_plugin
module
gpf.gpf_instance_plugin.gpf_instance_context_plugin
module
gpf.import_tools
module
gpf.import_tools.cli
module
gpf.import_tools.import_config
module
gpf.import_tools.import_tools
module
gpf.inmemory_storage
module
gpf.inmemory_storage.annotation_serialization
module
gpf.inmemory_storage.inmemory_genotype_storage
module
gpf.inmemory_storage.inmemory_import_storage
module
gpf.inmemory_storage.raw_variants
module
gpf.parquet
module
gpf.parquet.helpers
module
gpf.parquet.parquet_writer
module
gpf.parquet.partition_descriptor
module
gpf.parquet.schema2
module
gpf.parquet.schema2.annotate_schema2_parquet
module
gpf.parquet.schema2.loader
module
gpf.parquet.schema2.merge_parquet
module
gpf.parquet.schema2.parquet_io
module
gpf.parquet.schema2.processing_pipeline
module
gpf.parquet.schema2.serializers
module
gpf.parquet.schema2.variants_parquet_writer
module
gpf.parquet_storage
module
gpf.parquet_storage.storage
module
gpf.pedigrees
module
gpf.pedigrees.drawing
module
gpf.pedigrees.families_data
module
gpf.pedigrees.family
module
gpf.pedigrees.family_role_builder
module
gpf.pedigrees.family_tag_builder
module
gpf.pedigrees.layout
module
gpf.pedigrees.loader
module
gpf.pedigrees.pedigrees
module
gpf.pedigrees.testing
module
gpf.person_filters
module
gpf.person_filters.person_filters
module
gpf.person_sets
module
gpf.person_sets.person_sets
module
gpf.pheno
module
gpf.pheno.browser
module
gpf.pheno.build_pheno_browser
module
gpf.pheno.common
module
gpf.pheno.db
module
gpf.pheno.graphs
module
gpf.pheno.import_tools
module
gpf.pheno.pheno_data
module
gpf.pheno.pheno_import
module
gpf.pheno.prepare
module
gpf.pheno.prepare.measure_classifier
module
gpf.pheno.prepare_data
module
gpf.pheno.registry
module
gpf.pheno.storage
module
gpf.pheno.update_pheno_descriptions
module
gpf.pheno.utils
module
gpf.pheno.utils.commons
module
gpf.pheno.utils.lin_regress
module
gpf.pheno_tool
module
gpf.pheno_tool.pheno_tool_adapter
module
gpf.pheno_tool.tool
module
gpf.query_variants
module
gpf.query_variants.attribute_queries
module
gpf.query_variants.base_query_variants
module
gpf.query_variants.query_runners
module
gpf.query_variants.sql
module
gpf.query_variants.sql.schema2
module
gpf.query_variants.sql.schema2.base_query_builder
module
gpf.query_variants.sql.schema2.base_variants
module
gpf.query_variants.sql.schema2.family_builder
module
gpf.query_variants.sql.schema2.sql_query_builder
module
gpf.query_variants.sql.schema2.summary_builder
module
gpf.schema2_storage
module
gpf.schema2_storage.schema2_import_storage
module
gpf.schema2_storage.schema2_layout
module
gpf.studies
module
gpf.studies.study
module
gpf.studies.variants_db
module
gpf.testing
module
gpf.testing.acgt_import
module
gpf.testing.alla_import
module
gpf.testing.foobar_import
module
gpf.testing.import_helpers
module
gpf.testing.setup_helpers
module
gpf.testing.t4c8_import
module
gpf.tools
module
gpf.tools.dae2vcf
module
gpf.tools.dataset_helpers
module
gpf.tools.denovo2vcf
module
gpf.tools.draw_pedigree
module
gpf.tools.generate_common_report
module
gpf.tools.generate_denovo_gene_sets
module
gpf.tools.gpf_convert_study_config
module
gpf.tools.gpf_validation_runner
module
gpf.tools.grr_cache_repo
module
gpf.tools.liftover_tools
module
gpf.tools.ped2ped
module
gpf.tools.reannotate_instance
module
gpf.tools.simple_study_import
module
gpf.tools.to_gpf_gene_models_format
module
gpf.tools.vcf2tsv
module
gpf.utils
module
gpf.utils.testing
module
gpf.utils.variant_utils
module
gpf.variants
module
gpf.variants.attributes
module
gpf.variants.core
module
gpf.variants.family_variant
module
gpf.variants.variant
module
gpf.variants_loaders
module
gpf.variants_loaders.cnv
module
gpf.variants_loaders.cnv.flexible_cnv_loader
module
gpf.variants_loaders.cnv.loader
module
gpf.variants_loaders.dae
module
gpf.variants_loaders.dae.loader
module
gpf.variants_loaders.parquet
module
gpf.variants_loaders.parquet.loader
module
gpf.variants_loaders.raw
module
gpf.variants_loaders.raw.flexible_variant_loader
module
gpf.variants_loaders.raw.loader
module
gpf.variants_loaders.vcf
module
gpf.variants_loaders.vcf.loader
module
gpf.variants_loaders.vcf.serializer
module
gpf_fixture() (in module studies.tests.test_study_config_genotype_browser_columns)
(in module studies.tests.test_study_group_person_sets_queries)
gpf_instance
module
gpf_instance (gpf.pheno.common.PhenoImportConfig attribute)
gpf_instance.apps
module
gpf_instance.extension
module
gpf_instance.gpf_instance
module
gpf_instance.tests
module
gpf_instance.tests.test_genome_view
module
gpf_instance.tests.test_version_api
module
gpf_web
module
gpf_web.default_settings
module
gpf_web.eager_settings
module
gpf_web.gunicorn_settings
module
gpf_web.mypy_settings
module
gpf_web.remote_settings
module
gpf_web.settings
module
gpf_web.silk_settings
module
gpf_web.wdaemanage
module
gpf_web.wgpf
module
gpf_web.wgpf_settings
module
GPFConfigParser (class in gpf.configuration.gpf_config_parser)
GPFConfigValidator (class in gpf.configuration.gpf_config_parser)
GPFExtensionBase (class in gpf_instance.extension)
GPFInstance (class in gpf.gpf_instance)
(class in gpf.gpf_instance.gpf_instance)
GPFInstanceConfig (class in gpf.pheno.common)
GPFInstanceContextProvider (class in gpf.gpf_instance_plugin.gpf_instance_context_plugin)
GPFInstanceGenomicContext (class in gpf.gpf_instance_plugin.gpf_instance_context_plugin)
gpfjs
module
gpfjs.views
module
GPFOAuth2Authentication (class in utils.authentication)
GPFTool (class in gpf_instance.extension)
GPStatistic (class in gpf.gene_profile.statistic)
GraphColumn (class in gpf.pheno.graphs)
grey (gpf_web.default_settings.CustomFormatter attribute)
grouping() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method)
(gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method)
(gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method)
groups_api
module
groups_api.migrations
module
groups_api.tests
module
grr (gpf.gpf_instance.gpf_instance.GPFInstance property)
(gpf.gpf_instance.GPFInstance property)
grr() (in module enrichment_api.tests.conftest)
gt2str() (in module gpf.utils.variant_utils)
gt_flatten() (gpf.variants.family_variant.FamilyAllele method)
(gpf.variants.family_variant.FamilyVariant method)
H
half_sibling (gpf.variants.attributes.Role attribute)
handle() (users_api.management.commands.user_set_name.Command method)
(users_api.management.commands.user_setpasswd.Command method)
(users_api.management.commands.users_remove.Command method)
handle_measure_inference_tasks() (in module gpf.pheno.pheno_import)
has_affected_status_queries() (gpf.inmemory_storage.raw_variants.RawMemoryVariants method)
(gpf.parquet_storage.storage.ParquetLoaderVariants method)
(gpf.query_variants.base_query_variants.QueryVariants method)
(gpf.query_variants.base_query_variants.QueryVariantsBase method)
has_attr() (gpf.pedigrees.family.Person method)
has_attribute() (gpf.variants.family_variant.FamilyAllele method)
(gpf.variants.variant.SummaryAllele method)
(gpf.variants.variant.SummaryVariant method)
has_cnv (gpf.studies.study.GenotypeData property)
has_coding_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
has_complex (gpf.studies.study.GenotypeData property)
has_denovo (gpf.studies.study.GenotypeData property)
(gpf.studies.study.GenotypeDataGroup property)
has_denovo_variants() (gpf.import_tools.import_tools.ImportProject method)
has_family_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
has_family_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
has_frequency_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
has_gene_score() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
has_gene_set_collection() (gpf.gene_sets.gene_sets_db.GeneSetsDb method)
has_gene_sets() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method)
has_genotype_data (studies.study_wrapper.WDAEAbstractStudy property)
has_genotype_storage() (gpf.import_tools.import_tools.ImportProject method)
has_instrument_descriptions (gpf.pheno.browser.PhenoBrowser property)
has_measure() (gpf.pheno.pheno_data.PhenotypeData method)
has_measure_descriptions (gpf.pheno.browser.PhenoBrowser property)
has_members() (gpf.pedigrees.family.Family method)
has_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
has_pheno_data (studies.study_wrapper.WDAEAbstractStudy property)
has_phenotype_data() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
(gpf.pheno.registry.PhenoRegistry method)
has_region_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
has_summary_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
has_tag() (gpf.pedigrees.family.Person method)
has_transmitted (gpf.studies.study.GenotypeData property)
(gpf.studies.study.GenotypeDataGroup property)
has_variants() (gpf.import_tools.import_tools.ImportProject method)
(gpf.schema2_storage.schema2_layout.Schema2DatasetLayout method)
has_zygosity (gpf.studies.study.GenotypeData property)
help (gpf.genomic_scores.scores.ScoreDesc attribute)
(users_api.management.commands.user_set_name.Command attribute)
(users_api.management.commands.user_setpasswd.Command attribute)
(users_api.management.commands.users_remove.Command attribute)
heterozygous (gpf.variants.attributes.Zygosity attribute)
hist (gpf.genomic_scores.scores.ScoreDesc attribute)
histogram_configs (gpf.pheno.common.PhenoImportConfig attribute)
histogram_type (gpf.pheno.common.InferenceConfig attribute)
(gpf.pheno.prepare.measure_classifier.InferenceReport attribute)
homozygous (gpf.variants.attributes.Zygosity attribute)
I
id (gpf.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute)
(gpf.person_sets.person_sets.PersonSetCollectionConfig attribute)
(gpf.person_sets.person_sets.PersonSetConfig attribute)
(gpf.person_sets.PersonSetCollectionConfig attribute)
(gpf.person_sets.PersonSetConfig attribute)
(gpf.pheno.common.PhenoImportConfig attribute)
id_to_position (gpf.pedigrees.layout.Layout property)
import_config (gpf.pheno.common.ImportManifest attribute)
import_dataset() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method)
(gpf.parquet_storage.storage.ParquetGenotypeStorage method)
import_pheno_data() (in module gpf.pheno.pheno_import)
ImportConfigNormalizer (class in gpf.import_tools.import_tools)
ImportInstrument (class in gpf.pheno.pheno_import)
ImportManifest (class in gpf.pheno.common)
ImportProject (class in gpf.import_tools.import_tools)
ImportStorage (class in gpf.import_tools.import_tools)
include_reference (gpf.import_tools.import_tools.ImportProject property)
increase_indent() (gpf.configuration.study_config_builder.ConfigDumper method)
indel (gpf.variants.core.Allele.Type attribute)
index (gpf.import_tools.import_tools.Bucket attribute)
index() (in module gpfjs.views)
Individual (class in gpf.pedigrees.pedigrees)
individual_set() (gpf.pedigrees.pedigrees.Individual method)
(gpf.pedigrees.pedigrees.IndividualGroup method)
(gpf.pedigrees.pedigrees.MatingUnit method)
(gpf.pedigrees.pedigrees.SibshipUnit method)
IndividualGroup (class in gpf.pedigrees.pedigrees)
individuals_by_rank (gpf.pedigrees.layout.Layout property)
IndividualWithCoordinates (class in gpf.pedigrees.layout)
infer_measures() (in module gpf.pheno.pheno_import)
inference_config (gpf.pheno.common.PhenoImportConfig attribute)
inference_reference_impl() (in module gpf.pheno.prepare.measure_classifier)
inference_report (gpf.pheno.pheno_import.MeasureReport attribute)
InferenceConfig (class in gpf.pheno.common)
InferenceReport (class in gpf.pheno.prepare.measure_classifier)
Inheritance (class in gpf.variants.attributes)
inheritance() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
inheritance_in_members (gpf.variants.family_variant.FamilyAllele property)
init() (gpf.genotype_storage.genotype_storage_genomic_context_cli.CLIGenotypeStorageContextProvider method)
(gpf.gpf_instance_plugin.gpf_instance_context_plugin.GPFInstanceContextProvider method)
init_normalize_measures() (gpf.pheno_tool.tool.PhenoTool method)
init_vcf_loaders() (gpf.variants_loaders.vcf.loader.VcfLoader method)
initial (datasets_api.migrations.0001_initial.Migration attribute)
(user_queries.migrations.0001_initial.Migration attribute)
(users_api.migrations.0001_initial.Migration attribute)
InmemoryGenotypeStorage (class in gpf.inmemory_storage.inmemory_genotype_storage)
InmemoryImportStorage (class in gpf.inmemory_storage.inmemory_import_storage)
input_dir (gpf.import_tools.import_tools.ImportProject property)
(gpf.pheno.common.PhenoImportConfig attribute)
insert_gp() (gpf.gene_profile.db.GeneProfileDBWriter method)
insert_gps() (gpf.gene_profile.db.GeneProfileDBWriter method)
instance_path() (in module studies.tests.test_study_wrapper_person_sets)
(in module studies.tests.test_study_wrapper_unique_variants_query)
InstanceIdCommand (class in gpf.gpf_instance.adjustments.gpf_instance_adjustments)
Instrument (class in gpf.pheno.pheno_data)
instrument (gpf.pheno.common.DataDictionaryConfig attribute)
(gpf.pheno.common.InstrumentConfig attribute)
(gpf.pheno.common.InstrumentDictionaryConfig attribute)
instrument_column (gpf.pheno.common.DataDictionaryConfig attribute)
(gpf.pheno.common.InstrumentDictionaryConfig attribute)
instrument_dictionary (gpf.pheno.common.PhenoImportConfig attribute)
instrument_files (gpf.pheno.common.PhenoImportConfig attribute)
instrument_name (gpf.pheno.common.RegressionMeasure attribute)
(gpf.pheno.pheno_import.MeasureReport attribute)
InstrumentConfig (class in gpf.pheno.common)
InstrumentDescriptionsConfig (class in gpf.pheno.common)
InstrumentDictionaryConfig (class in gpf.pheno.common)
instruments (gpf.pheno.pheno_data.PhenotypeData property)
int_type() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method)
(gpf.query_variants.sql.schema2.base_query_builder.Dialect static method)
intersection() (gpf.pedigrees.pedigrees.Interval method)
Interval (class in gpf.pedigrees.pedigrees)
IntervalForVertex (class in gpf.pedigrees.pedigrees)
inverse_curve_p1() (gpf.pedigrees.layout.Line method)
inverse_curve_p2() (gpf.pedigrees.layout.Line method)
inverse_curve_y_at() (gpf.pedigrees.layout.Line method)
is_active_vertex() (gpf.pedigrees.pedigrees.Realization method)
is_all_reference_genotype() (in module gpf.utils.variant_utils)
is_all_unknown_genotype() (in module gpf.utils.variant_utils)
is_browser_outdated() (gpf.pheno.pheno_data.PhenotypeData method)
is_cached() (gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method)
is_closed() (gpf.query_variants.query_runners.QueryRunner method)
is_cnv() (gpf.variants.core.Allele.Type class method)
is_connected() (gpf.pedigrees.pedigrees.FamilyConnections method)
is_convertible_to_numeric() (in module gpf.pheno.prepare.measure_classifier)
is_done() (gpf.query_variants.query_runners.QueryResult method)
(gpf.query_variants.query_runners.QueryRunner method)
is_email_valid() (in module utils.email_regex)
is_empty() (gpf.common_reports.denovo_report.DenovoReport method)
(gpf.common_reports.denovo_report.DenovoReportTable method)
(gpf.common_reports.denovo_report.EffectCell method)
(gpf.common_reports.people_counter.PeopleCounter method)
(gpf.parquet.partition_descriptor.Partition method)
(gpf.query_variants.sql.schema2.sql_query_builder.QueryHeuristics method)
is_empty_field() (gpf.common_reports.people_counter.PeopleCounter method)
is_genotype (studies.study_wrapper.WDAEAbstractStudy property)
is_group (gpf.pheno.pheno_data.PhenotypeData property)
(gpf.pheno.pheno_data.PhenotypeGroup property)
(gpf.studies.study.GenotypeData property)
(gpf.studies.study.GenotypeDataGroup property)
(gpf.studies.study.GenotypeDataStudy property)
(studies.study_wrapper.WDAEAbstractStudy property)
is_in_interval_order() (gpf.pedigrees.pedigrees.Realization method)
is_individual() (gpf.pedigrees.pedigrees.Individual method)
(gpf.pedigrees.pedigrees.IndividualGroup method)
is_loaded() (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground method)
(gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method)
(gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method)
(gpf.enrichment_tool.samocha_background.SamochaEnrichmentBackground method)
is_maximal() (gpf.pedigrees.pedigrees.Realization method)
is_nan() (in module gpf.pheno.prepare.measure_classifier)
is_numeric() (gpf.pheno.common.MeasureType static method)
is_older_than() (gpf.pheno.common.ImportManifest method)
is_password_valid() (in module utils.password_requirements)
is_pedigree_only() (gpf.person_sets.person_sets.PersonSetCollection method)
(gpf.person_sets.PersonSetCollection method)
is_phenotype (studies.study_wrapper.WDAEAbstractStudy property)
is_read_only() (gpf.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method)
(gpf.genotype_storage.genotype_storage.GenotypeStorage method)
is_reference() (gpf.variants.family_variant.FamilyVariant method)
is_reference_allele (gpf.variants.variant.SummaryAllele property)
is_reference_genotype() (in module gpf.utils.variant_utils)
is_row_empty() (gpf.common_reports.denovo_report.EffectRow method)
is_started() (gpf.query_variants.query_runners.QueryRunner method)
is_text() (gpf.pheno.common.MeasureType static method)
is_tr() (gpf.variants.core.Allele.Type class method)
is_unknown() (gpf.variants.family_variant.FamilyVariant method)
is_unknown_genotype() (in module gpf.utils.variant_utils)
is_valid_family() (gpf.pedigrees.pedigrees.FamilyConnections static method)
items() (gpf.pedigrees.families_data.FamiliesData method)
iterator_to_json() (in module utils.streaming_response_util)
J
jitter (gpf.pheno.common.RegressionMeasure attribute)
join_base_url_and_parquet_scan() (in module gpf.duckdb_storage.duckdb_storage_helpers)
join_pheno_df_with_variants() (gpf.pheno_tool.tool.PhenoTool static method)
JsonVariantsDataSerializer (class in gpf.parquet.schema2.serializers)
K
keys() (gpf.pedigrees.families_data.FamiliesData method)
L
label (gpf.pedigrees.family.FamilyTag property)
(gpf.pheno.graphs.GraphColumn property)
large_deletion (gpf.variants.core.Allele.Type attribute)
LARGE_DPI (gpf.pheno.prepare_data.PreparePhenoBrowserBase attribute)
large_duplication (gpf.variants.core.Allele.Type attribute)
large_values_desc (gpf.genomic_scores.scores.ScoreDesc attribute)
Layout (class in gpf.pedigrees.layout)
layout (gpf.pedigrees.family.Person property)
Layout.BBox (class in gpf.pedigrees.layout)
layout_parser() (in module gpf.pedigrees.layout)
legend_json() (gpf.person_sets.person_sets.PersonSetCollection method)
(gpf.person_sets.PersonSetCollection method)
liftover_variants() (gpf.tools.liftover_tools.CNVLiftoverTool method)
(gpf.tools.liftover_tools.DaeLiftoverTool method)
(gpf.tools.liftover_tools.DenovoLiftoverTool method)
(gpf.tools.liftover_tools.LiftoverTool method)
(gpf.tools.liftover_tools.VCFLiftoverTool method)
LiftoverTool (class in gpf.tools.liftover_tools)
Line (class in gpf.pedigrees.layout)
LinearRegression (class in gpf.pheno.utils.lin_regress)
list_gp_gene_symbols() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
list_symbols() (gpf.gene_profile.db.GeneProfileDB method)
literal() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method)
(gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method)
(gpf.query_variants.attribute_queries.AttributeQueryTransformerSQLLegacy method)
(gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method)
load() (gpf.common_reports.common_report.CommonReport static method)
(gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground method)
(gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground method)
(gpf.enrichment_tool.gene_weights_background.GeneWeightsEnrichmentBackground method)
(gpf.enrichment_tool.samocha_background.SamochaEnrichmentBackground method)
(gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method)
(gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
(gpf.pedigrees.loader.FamiliesLoader method)
load_collection() (gpf.gene_sets.denovo_gene_set_helpers.DenovoGeneSetHelpers class method)
load_collection_from_dict() (gpf.gene_sets.denovo_gene_set_helpers.DenovoGeneSetHelpers class method)
load_config() (gpf.configuration.gpf_config_parser.GPFConfigParser class method)
load_config_dict() (gpf.configuration.gpf_config_parser.GPFConfigParser class method)
load_config_raw() (gpf.configuration.gpf_config_parser.GPFConfigParser class method)
load_directory_configs() (gpf.configuration.gpf_config_parser.GPFConfigParser class method)
load_from_dir() (gpf.parquet.schema2.loader.ParquetLoader static method)
load_histogram_configs() (in module gpf.pheno.pheno_import)
load_inference_configs() (in module gpf.pheno.pheno_import)
load_instrument_description_file() (in module gpf.pheno.pheno_import)
load_instrument_descriptions() (in module gpf.pheno.pheno_import)
load_measure_description_file() (in module gpf.pheno.pheno_import)
load_measure_descriptions() (in module gpf.pheno.pheno_import)
load_meta() (gpf.schema2_storage.schema2_import_storage.Schema2ImportStorage static method)
load_object() (in module query_state_save.tests.conftest)
load_pedigree_file() (gpf.pedigrees.loader.FamiliesLoader static method)
load_schema2_dataset_layout() (in module gpf.schema2_storage.schema2_layout)
load_simple_families_file() (gpf.pedigrees.loader.FamiliesLoader static method)
load_study_config() (in module gpf.tools.gpf_convert_study_config)
loaded_variants (gpf.genotype_storage.genotype_storage.GenotypeStorage property)
location (gpf.variants.variant.SummaryVariant property)
location_variant_to_vcf_transformer() (in module gpf.variants_loaders.raw.flexible_variant_loader)
log_filter() (in module utils.logger)
M
M (gpf.variants.attributes.Sex attribute)
main() (gpf.tools.gpf_validation_runner.MainRunner method)
(in module gpf.gene_profile.convert_gene_profile_to_duckdb)
(in module gpf.gene_profile.generate_gene_profile)
(in module gpf.import_tools.cli)
(in module gpf.pheno.build_pheno_browser)
(in module gpf.pheno.import_tools)
(in module gpf.pheno.pheno_import)
(in module gpf.pheno.update_pheno_descriptions)
(in module gpf.tools.dae2vcf)
(in module gpf.tools.denovo2vcf)
(in module gpf.tools.draw_pedigree)
(in module gpf.tools.generate_common_report)
(in module gpf.tools.generate_denovo_gene_sets)
(in module gpf.tools.gpf_convert_study_config)
(in module gpf.tools.gpf_validation_runner)
(in module gpf.tools.ped2ped)
(in module gpf.tools.simple_study_import)
(in module gpf.tools.to_gpf_gene_models_format)
(in module gpf.tools.vcf2tsv)
(in module gpf_web.wdaemanage)
MainRunner (class in gpf.tools.gpf_validation_runner)
make_all_region_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
make_coding_bin() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
make_config() (studies.study_wrapper.WDAEAbstractStudy static method)
make_family_bin() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
make_frequency_bin() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
make_pedigree_filter() (in module gpf.person_filters)
(in module gpf.person_filters.person_filters)
make_pheno_filter() (in module gpf.person_filters)
(in module gpf.person_filters.person_filters)
make_pheno_filter_beta() (in module gpf.person_filters)
(in module gpf.person_filters.person_filters)
make_query_transformer() (in module studies.query_transformer)
make_region_bin() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
make_region_bins_regions() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
make_response_transformer() (in module studies.response_transformer)
make_tool() (common_reports_api.common_reports_helper.CommonReportsHelper static method)
(enrichment_api.enrichment_builder.EnrichmentBuilder static method)
(enrichment_api.enrichment_helper.EnrichmentHelper static method)
(gpf_instance.extension.GPFTool static method)
(pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper static method)
(pheno_tool_api.adapter.PhenoToolAdapter static method)
make_validation_runner() (gpf.tools.gpf_validation_runner.MainRunner method)
male (gpf.enrichment_tool.event_counters.EnrichmentResult attribute)
(gpf.enrichment_tool.event_counters.EventCountersResult attribute)
(gpf.enrichment_tool.event_counters.EventsResult attribute)
(gpf.enrichment_tool.event_counters.VariantEventsResult attribute)
(gpf.person_sets.ChildrenBySex attribute)
(gpf.person_sets.ChildrenStats attribute)
(gpf.person_sets.person_sets.ChildrenBySex attribute)
(gpf.person_sets.person_sets.ChildrenStats attribute)
(gpf.variants.attributes.Sex attribute)
male_female_legend() (in module gpf.pheno.graphs)
MALE_PRB (gpf.pedigrees.family.FamilyTag attribute)
males_count() (gpf.pheno.graphs.GraphColumn method)
mat2str() (in module gpf.utils.variant_utils)
matched_alleles (gpf.variants.variant.SummaryVariant property)
matched_alleles_indexes (gpf.variants.variant.SummaryVariant property)
matched_gene_effects (gpf.variants.variant.SummaryVariant property)
Matcher (class in gpf.query_variants.attribute_queries)
maternal_aunt (gpf.variants.attributes.Role attribute)
maternal_cousin (gpf.variants.attributes.Role attribute)
maternal_grandfather (gpf.variants.attributes.Role attribute)
maternal_grandmother (gpf.variants.attributes.Role attribute)
maternal_half_sibling (gpf.variants.attributes.Role attribute)
maternal_uncle (gpf.variants.attributes.Role attribute)
Mating (class in gpf.pedigrees.family_role_builder)
MatingUnit (class in gpf.pedigrees.pedigrees)
MAX_CHILD_NUMBER (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute)
max_rank (gpf.pheno.common.RankRange attribute)
max_rank() (gpf.pedigrees.pedigrees.FamilyConnections method)
max_value (gpf.pheno.prepare.measure_classifier.InferenceReport attribute)
max_x (gpf.pedigrees.layout.Layout.BBox attribute)
max_y (gpf.pedigrees.layout.Layout.BBox attribute)
Measure (class in gpf.pheno.pheno_data)
measure_column (gpf.pheno.common.DataDictionaryConfig attribute)
measure_name (gpf.pheno.pheno_import.MeasureReport attribute)
measure_names (gpf.pheno.common.RegressionMeasure attribute)
measure_type (gpf.pheno.pheno_import.MeasureReport attribute)
MeasureDescriptionsConfig (class in gpf.pheno.common)
MeasureHistogramConfigs (class in gpf.pheno.common)
MeasureReport (class in gpf.pheno.pheno_import)
measures (gpf.pheno.pheno_data.PhenotypeData property)
measures_api
module
measures_api.tests
module
measures_api.tests.test_measures_api
module
measures_count_status() (pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method)
(pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method)
MeasureType (class in gpf.pheno.common)
media_type (sentry.views.PlainTextParser attribute)
member_fpids (gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
member_has_both_parents() (gpf.pedigrees.family.Family method)
member_has_dad() (gpf.pedigrees.family.Family method)
member_has_mom() (gpf.pedigrees.family.Family method)
member_has_parent() (gpf.pedigrees.family.Family method)
member_ids (gpf.pedigrees.family.Family property)
(gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
member_index (gpf.pedigrees.family.Person property)
member_is_child() (gpf.pedigrees.family.Family method)
member_is_parent() (gpf.pedigrees.family.Family method)
members (gpf.pedigrees.pedigrees.FamilyConnections property)
members_in_order (gpf.pedigrees.family.Family property)
members_in_order_get_family_structure() (in module studies.response_transformer)
members_index() (gpf.pedigrees.family.Family method)
memory_limit (gpf.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute)
mendelian (gpf.variants.attributes.Inheritance attribute)
merge_config() (gpf.configuration.gpf_config_parser.GPFConfigParser static method)
merge_configs() (gpf.person_sets.person_sets.PersonSetCollection static method)
(gpf.person_sets.PersonSetCollection static method)
merge_families() (in module gpf.pedigrees.families_data)
merge_histogram_configs() (in module gpf.pheno.pheno_import)
merge_inference_configs() (in module gpf.pheno.pheno_import)
merge_parquet_directory() (in module gpf.parquet.schema2.merge_parquet)
merge_parquets() (in module gpf.parquet.helpers)
(in module gpf.parquet.schema2.merge_parquet)
merge_partitions() (in module gpf.parquet.schema2.annotate_schema2_parquet)
merge_variants_parquets() (in module gpf.parquet.parquet_writer)
(in module gpf.parquet.schema2.merge_parquet)
meta (gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute)
(gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute)
Migration (class in datasets_api.migrations.0001_initial)
(class in datasets_api.migrations.0002_dataset_groups)
(class in datasets_api.migrations.0003_alter_dataset_options)
(class in datasets_api.migrations.0004_dataset_broken)
(class in datasets_api.migrations.0005_dataset_dataset_name)
(class in datasets_api.migrations.0006_datasethierarchy)
(class in datasets_api.migrations.0007_datasethierarchy_direct)
(class in datasets_api.migrations.0008_datasethierarchy_instance_id)
(class in query_state_save.migrations.0001_initial)
(class in query_state_save.migrations.0002_auto_20190205_0736)
(class in query_state_save.migrations.0003_querystate_origin_querystate_timestamp)
(class in user_queries.migrations.0001_initial)
(class in users_api.migrations.0001_initial)
(class in users_api.migrations.0002_auto_20190424_0751)
(class in users_api.migrations.0003_authenticationlog)
(class in users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more)
(class in users_api.migrations.0005_gpuserstate)
min_individuals (gpf.pheno.common.InferenceConfig attribute)
(gpf.pheno.prepare.measure_classifier.InferenceReport attribute)
min_rank (gpf.pheno.common.RankRange attribute)
min_value (gpf.pheno.prepare.measure_classifier.InferenceReport attribute)
min_x (gpf.pedigrees.layout.Layout.BBox attribute)
min_y (gpf.pedigrees.layout.Layout.BBox attribute)
missing (gpf.pedigrees.family.Person property)
(gpf.variants.attributes.Inheritance attribute)
MISSING_DAD (gpf.pedigrees.family.FamilyTag attribute)
MISSING_MOM (gpf.pedigrees.family.FamilyTag attribute)
mock_instance() (in module gpf_instance.tests.test_version_api)
model_computed_fields (gpf.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute)
(gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute)
(gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute)
(gpf.gene_sets.denovo_gene_sets_config.DGSSpec attribute)
(gpf.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.SexesCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute)
(gpf.person_sets.person_sets.PersonSetCollectionConfig attribute)
(gpf.person_sets.person_sets.PersonSetConfig attribute)
(gpf.person_sets.person_sets.SourceConfig attribute)
(gpf.person_sets.PersonSetCollectionConfig attribute)
(gpf.person_sets.PersonSetConfig attribute)
(gpf.person_sets.SourceConfig attribute)
(gpf.pheno.common.DataDictionaryConfig attribute)
(gpf.pheno.common.DestinationConfig attribute)
(gpf.pheno.common.GPFInstanceConfig attribute)
(gpf.pheno.common.ImportManifest attribute)
(gpf.pheno.common.InferenceConfig attribute)
(gpf.pheno.common.InstrumentConfig attribute)
(gpf.pheno.common.InstrumentDescriptionsConfig attribute)
(gpf.pheno.common.InstrumentDictionaryConfig attribute)
(gpf.pheno.common.MeasureDescriptionsConfig attribute)
(gpf.pheno.common.MeasureHistogramConfigs attribute)
(gpf.pheno.common.PhenoImportConfig attribute)
(gpf.pheno.common.RankRange attribute)
(gpf.pheno.common.RegressionMeasure attribute)
(gpf.pheno.common.StudyConfig attribute)
(gpf.pheno.pheno_import.MeasureReport attribute)
(gpf.pheno.prepare.measure_classifier.InferenceReport attribute)
(gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute)
(gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute)
model_config (gpf.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute)
(gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute)
(gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute)
(gpf.gene_sets.denovo_gene_sets_config.DGSSpec attribute)
(gpf.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.SexesCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute)
(gpf.person_sets.person_sets.PersonSetCollectionConfig attribute)
(gpf.person_sets.person_sets.PersonSetConfig attribute)
(gpf.person_sets.person_sets.SourceConfig attribute)
(gpf.person_sets.PersonSetCollectionConfig attribute)
(gpf.person_sets.PersonSetConfig attribute)
(gpf.person_sets.SourceConfig attribute)
(gpf.pheno.common.DataDictionaryConfig attribute)
(gpf.pheno.common.DestinationConfig attribute)
(gpf.pheno.common.GPFInstanceConfig attribute)
(gpf.pheno.common.ImportManifest attribute)
(gpf.pheno.common.InferenceConfig attribute)
(gpf.pheno.common.InstrumentConfig attribute)
(gpf.pheno.common.InstrumentDescriptionsConfig attribute)
(gpf.pheno.common.InstrumentDictionaryConfig attribute)
(gpf.pheno.common.MeasureDescriptionsConfig attribute)
(gpf.pheno.common.MeasureHistogramConfigs attribute)
(gpf.pheno.common.PhenoImportConfig attribute)
(gpf.pheno.common.RankRange attribute)
(gpf.pheno.common.RegressionMeasure attribute)
(gpf.pheno.common.StudyConfig attribute)
(gpf.pheno.pheno_import.MeasureReport attribute)
(gpf.pheno.prepare.measure_classifier.InferenceReport attribute)
(gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute)
(gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute)
model_fields (gpf.duckdb_storage.duckdb_storage_config.DuckDbBaseConf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute)
(gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute)
(gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute)
(gpf.gene_sets.denovo_gene_sets_config.DGSSpec attribute)
(gpf.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.SexesCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute)
(gpf.person_sets.person_sets.PersonSetCollectionConfig attribute)
(gpf.person_sets.person_sets.PersonSetConfig attribute)
(gpf.person_sets.person_sets.SourceConfig attribute)
(gpf.person_sets.PersonSetCollectionConfig attribute)
(gpf.person_sets.PersonSetConfig attribute)
(gpf.person_sets.SourceConfig attribute)
(gpf.pheno.common.DataDictionaryConfig attribute)
(gpf.pheno.common.DestinationConfig attribute)
(gpf.pheno.common.GPFInstanceConfig attribute)
(gpf.pheno.common.ImportManifest attribute)
(gpf.pheno.common.InferenceConfig attribute)
(gpf.pheno.common.InstrumentConfig attribute)
(gpf.pheno.common.InstrumentDescriptionsConfig attribute)
(gpf.pheno.common.InstrumentDictionaryConfig attribute)
(gpf.pheno.common.MeasureDescriptionsConfig attribute)
(gpf.pheno.common.MeasureHistogramConfigs attribute)
(gpf.pheno.common.PhenoImportConfig attribute)
(gpf.pheno.common.RankRange attribute)
(gpf.pheno.common.RegressionMeasure attribute)
(gpf.pheno.common.StudyConfig attribute)
(gpf.pheno.pheno_import.MeasureReport attribute)
(gpf.pheno.prepare.measure_classifier.InferenceReport attribute)
(gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute)
(gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute)
modify_tuple() (gpf.configuration.gpf_config_parser.GPFConfigParser class method)
module
common_reports_api
common_reports_api.common_reports_helper
common_reports_api.tests
common_reports_api.tests.test_common_reports_api
datasets_api
datasets_api.migrations
datasets_api.migrations.0001_initial
datasets_api.migrations.0002_dataset_groups
datasets_api.migrations.0003_alter_dataset_options
datasets_api.migrations.0004_dataset_broken
datasets_api.migrations.0005_dataset_dataset_name
datasets_api.migrations.0006_datasethierarchy
datasets_api.migrations.0007_datasethierarchy_direct
datasets_api.migrations.0008_datasethierarchy_instance_id
datasets_api.tests
datasets_api.tests.conftest
enrichment_api
enrichment_api.enrichment_builder
enrichment_api.enrichment_helper
enrichment_api.enrichment_serializer
enrichment_api.tests
enrichment_api.tests.conftest
enrichment_api.tests.test_enrichment_api
enrichment_api.tests.test_enrichment_builder
enrichment_api.tests.test_enrichment_helper_simple
enrichment_api.tests.test_enrichment_serializer
enrichment_api.tests.test_t4c8_enrichment
family_api
family_api.tests
family_api.tests.test_family_api
gene_profiles_api
gene_profiles_api.tests
gene_profiles_api.tests.test_agp_api
gene_profiles_api.tests.test_agp_api_configless
gene_scores
gene_scores.tests
gene_scores.tests.conftest
gene_scores.tests.test_gene_scores
gene_scores.tests.test_gene_scores_db
gene_scores.tests.test_gene_scores_views
gene_scores.tests.test_scores_partitions
gene_sets
gene_sets.tests
gene_sets.tests.test_gene_sets_api
gene_view
gene_view.tests
gene_view.tests.test_gene_view
genomes_api
genomes_api.tests
genomes_api.tests.test_gene_models_api
genomic_scores_api
genomic_scores_api.tests
genomic_scores_api.tests.test_genomic_scores_api
genotype_browser
genotype_browser.tests
genotype_browser.tests.conftest
genotype_browser.tests.test_effect_types_download
genotype_browser.tests.test_pheno_columns
genotype_browser.tests.test_pheno_filters
gpf
gpf.common_reports
gpf.common_reports.common_report
gpf.common_reports.denovo_report
gpf.common_reports.family_counter
gpf.common_reports.family_report
gpf.common_reports.people_counter
gpf.configuration
gpf.configuration.gpf_config_parser
gpf.configuration.schemas
gpf.configuration.schemas.dae_conf
gpf.configuration.schemas.gene_profile
gpf.configuration.schemas.gene_weights_db
gpf.configuration.schemas.person_sets
gpf.configuration.schemas.phenotype_data
gpf.configuration.schemas.study_config
gpf.configuration.schemas.wdae_study_config
gpf.configuration.study_config_builder
gpf.configuration.utils
gpf.duckdb_storage
gpf.duckdb_storage.duckdb2_variants
gpf.duckdb_storage.duckdb_connection_factory
gpf.duckdb_storage.duckdb_genotype_storage
gpf.duckdb_storage.duckdb_import_storage
gpf.duckdb_storage.duckdb_legacy_genotype_storage
gpf.duckdb_storage.duckdb_storage_config
gpf.duckdb_storage.duckdb_storage_helpers
gpf.duckdb_storage.duckdb_variants
gpf.enrichment_tool
gpf.enrichment_tool.base_enrichment_background
gpf.enrichment_tool.build_coding_length_enrichment_background
gpf.enrichment_tool.build_ur_synonymous_enrichment_background
gpf.enrichment_tool.enrichment_cache_builder
gpf.enrichment_tool.enrichment_utils
gpf.enrichment_tool.event_counters
gpf.enrichment_tool.gene_weights_background
gpf.enrichment_tool.genotype_helper
gpf.enrichment_tool.resource_implementations
gpf.enrichment_tool.resource_implementations.enrichment_resource_impl
gpf.enrichment_tool.samocha_background
gpf.gene_profile
gpf.gene_profile.convert_gene_profile_to_duckdb
gpf.gene_profile.db
gpf.gene_profile.exporter
gpf.gene_profile.generate_gene_profile
gpf.gene_profile.statistic
gpf.gene_sets
gpf.gene_sets.denovo_gene_set_collection
gpf.gene_sets.denovo_gene_set_helpers
gpf.gene_sets.denovo_gene_sets_config
gpf.gene_sets.denovo_gene_sets_db
gpf.gene_sets.gene_sets_db
gpf.genomic_scores
gpf.genomic_scores.scores
gpf.genotype_storage
gpf.genotype_storage.genotype_storage
gpf.genotype_storage.genotype_storage_genomic_context_cli
gpf.genotype_storage.genotype_storage_registry
gpf.gpf_instance
gpf.gpf_instance.adjustments
gpf.gpf_instance.adjustments.adjust_command
gpf.gpf_instance.adjustments.adjust_duckdb_storage
gpf.gpf_instance.adjustments.adjust_impala_storage
gpf.gpf_instance.adjustments.gpf_instance_adjustments
gpf.gpf_instance.gpf_instance
gpf.gpf_instance_plugin
gpf.gpf_instance_plugin.gpf_instance_context_plugin
gpf.import_tools
gpf.import_tools.cli
gpf.import_tools.import_config
gpf.import_tools.import_tools
gpf.inmemory_storage
gpf.inmemory_storage.annotation_serialization
gpf.inmemory_storage.inmemory_genotype_storage
gpf.inmemory_storage.inmemory_import_storage
gpf.inmemory_storage.raw_variants
gpf.parquet
gpf.parquet.helpers
gpf.parquet.parquet_writer
gpf.parquet.partition_descriptor
gpf.parquet.schema2
gpf.parquet.schema2.annotate_schema2_parquet
gpf.parquet.schema2.loader
gpf.parquet.schema2.merge_parquet
gpf.parquet.schema2.parquet_io
gpf.parquet.schema2.processing_pipeline
gpf.parquet.schema2.serializers
gpf.parquet.schema2.variants_parquet_writer
gpf.parquet_storage
gpf.parquet_storage.storage
gpf.pedigrees
gpf.pedigrees.drawing
gpf.pedigrees.families_data
gpf.pedigrees.family
gpf.pedigrees.family_role_builder
gpf.pedigrees.family_tag_builder
gpf.pedigrees.layout
gpf.pedigrees.loader
gpf.pedigrees.pedigrees
gpf.pedigrees.testing
gpf.person_filters
gpf.person_filters.person_filters
gpf.person_sets
gpf.person_sets.person_sets
gpf.pheno
gpf.pheno.browser
gpf.pheno.build_pheno_browser
gpf.pheno.common
gpf.pheno.db
gpf.pheno.graphs
gpf.pheno.import_tools
gpf.pheno.pheno_data
gpf.pheno.pheno_import
gpf.pheno.prepare
gpf.pheno.prepare.measure_classifier
gpf.pheno.prepare_data
gpf.pheno.registry
gpf.pheno.storage
gpf.pheno.update_pheno_descriptions
gpf.pheno.utils
gpf.pheno.utils.commons
gpf.pheno.utils.lin_regress
gpf.pheno_tool
gpf.pheno_tool.pheno_tool_adapter
gpf.pheno_tool.tool
gpf.query_variants
gpf.query_variants.attribute_queries
gpf.query_variants.base_query_variants
gpf.query_variants.query_runners
gpf.query_variants.sql
gpf.query_variants.sql.schema2
gpf.query_variants.sql.schema2.base_query_builder
gpf.query_variants.sql.schema2.base_variants
gpf.query_variants.sql.schema2.family_builder
gpf.query_variants.sql.schema2.sql_query_builder
gpf.query_variants.sql.schema2.summary_builder
gpf.schema2_storage
gpf.schema2_storage.schema2_import_storage
gpf.schema2_storage.schema2_layout
gpf.studies
gpf.studies.study
gpf.studies.variants_db
gpf.testing
gpf.testing.acgt_import
gpf.testing.alla_import
gpf.testing.foobar_import
gpf.testing.import_helpers
gpf.testing.setup_helpers
gpf.testing.t4c8_import
gpf.tools
gpf.tools.dae2vcf
gpf.tools.dataset_helpers
gpf.tools.denovo2vcf
gpf.tools.draw_pedigree
gpf.tools.generate_common_report
gpf.tools.generate_denovo_gene_sets
gpf.tools.gpf_convert_study_config
gpf.tools.gpf_validation_runner
gpf.tools.grr_cache_repo
gpf.tools.liftover_tools
gpf.tools.ped2ped
gpf.tools.reannotate_instance
gpf.tools.simple_study_import
gpf.tools.to_gpf_gene_models_format
gpf.tools.vcf2tsv
gpf.utils
gpf.utils.testing
gpf.utils.variant_utils
gpf.variants
gpf.variants.attributes
gpf.variants.core
gpf.variants.family_variant
gpf.variants.variant
gpf.variants_loaders
gpf.variants_loaders.cnv
gpf.variants_loaders.cnv.flexible_cnv_loader
gpf.variants_loaders.cnv.loader
gpf.variants_loaders.dae
gpf.variants_loaders.dae.loader
gpf.variants_loaders.parquet
gpf.variants_loaders.parquet.loader
gpf.variants_loaders.raw
gpf.variants_loaders.raw.flexible_variant_loader
gpf.variants_loaders.raw.loader
gpf.variants_loaders.vcf
gpf.variants_loaders.vcf.loader
gpf.variants_loaders.vcf.serializer
gpf_instance
gpf_instance.apps
gpf_instance.extension
gpf_instance.gpf_instance
gpf_instance.tests
gpf_instance.tests.test_genome_view
gpf_instance.tests.test_version_api
gpf_web
gpf_web.default_settings
gpf_web.eager_settings
gpf_web.gunicorn_settings
gpf_web.mypy_settings
gpf_web.remote_settings
gpf_web.settings
gpf_web.silk_settings
gpf_web.wdaemanage
gpf_web.wgpf
gpf_web.wgpf_settings
gpfjs
gpfjs.views
groups_api
groups_api.migrations
groups_api.tests
measures_api
measures_api.tests
measures_api.tests.test_measures_api
person_sets_api
person_sets_api.tests
person_sets_api.tests.test_person_sets_api
pheno_browser_api
pheno_browser_api.pheno_browser_helper
pheno_browser_api.tests
pheno_tool_api
pheno_tool_api.adapter
pheno_tool_api.tests
pheno_tool_api.tests.test_pheno_tool_api
query_base
query_state_save
query_state_save.migrations
query_state_save.migrations.0001_initial
query_state_save.migrations.0002_auto_20190205_0736
query_state_save.migrations.0003_querystate_origin_querystate_timestamp
query_state_save.tests
query_state_save.tests.conftest
sentry
sentry.tests
sentry.tests.test_sentry
sentry.urls
sentry.views
studies
studies.conftest
studies.query_transformer
studies.response_transformer
studies.study_wrapper
studies.tests
studies.tests.test_pheno_measures_columns
studies.tests.test_query_transformer
studies.tests.test_query_transformer_family_tags
studies.tests.test_query_transformer_present_in_child_and_parent
studies.tests.test_response_transformer_columns
studies.tests.test_study_config_genotype_browser_columns
studies.tests.test_study_group_person_sets_queries
studies.tests.test_study_query_request
studies.tests.test_study_wrapper
studies.tests.test_study_wrapper_person_sets
studies.tests.test_study_wrapper_queries
studies.tests.test_study_wrapper_unique_variants_query
user_queries
user_queries.migrations
user_queries.migrations.0001_initial
users_api
users_api.management
users_api.management.commands
users_api.management.commands.user_set_name
users_api.management.commands.user_setpasswd
users_api.management.commands.users_remove
users_api.migrations
users_api.migrations.0001_initial
users_api.migrations.0002_auto_20190424_0751
users_api.migrations.0003_authenticationlog
users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more
users_api.migrations.0005_gpuserstate
users_api.tests
utils
utils.authentication
utils.datasets
utils.email_regex
utils.expand_gene_set
utils.gene_sets
utils.logger
utils.pagination
utils.password_requirements
utils.query_params
utils.streaming_response_util
utils.testing
mom (gpf.variants.attributes.Role attribute)
MULTIPLEX (gpf.pedigrees.family.FamilyTag attribute)
MultiReader (class in gpf.parquet.schema2.loader)
N
name (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property)
(gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentResourceBackground property)
(gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property)
(gpf.enrichment_tool.samocha_background.SamochaEnrichmentBackground property)
(gpf.gene_sets.denovo_gene_sets_config.EffectsCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.SexesCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute)
(gpf.genomic_scores.scores.ScoreDesc attribute)
(gpf.person_sets.person_sets.PersonSetCollectionConfig attribute)
(gpf.person_sets.person_sets.PersonSetConfig attribute)
(gpf.person_sets.PersonSetCollectionConfig attribute)
(gpf.person_sets.PersonSetConfig attribute)
(gpf.pheno.pheno_import.ImportInstrument attribute)
(gpf.studies.study.GenotypeData property)
(gpf_instance.apps.WDAEConfig attribute)
(studies.study_wrapper.WDAEAbstractStudy property)
name_in_gene_sets() (in module gene_sets.tests.test_gene_sets_api)
nan (gpf.pheno.prepare.measure_classifier.Convertible attribute)
neg() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method)
(gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method)
(gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method)
NO_RANK (gpf.pedigrees.pedigrees.Individual attribute)
NOBODY_INTEREST_LOG_INTERVAL (gpf.query_variants.query_runners.QueryRunner attribute)
NOBODY_INTEREST_THRESHOLD (gpf.query_variants.query_runners.QueryRunner attribute)
non_numeric (gpf.pheno.prepare.measure_classifier.Convertible attribute)
non_numeric_cutoff (gpf.pheno.common.InferenceConfig attribute)
normalization_rules (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute)
normalize() (gpf.import_tools.import_tools.ImportConfigNormalizer method)
not_role() (gpf.variants.attributes.Role static method)
not_sequenced (gpf.pedigrees.family.Person property)
NOTSET (gpf.tools.gpf_validation_runner.TestStatus attribute)
NUCLEAR (gpf.pedigrees.family.FamilyTag attribute)
number_config (gpf.pheno.common.MeasureHistogramConfigs attribute)
number_of_children_with_event (gpf.common_reports.denovo_report.EffectCell property)
number_of_observed_events (gpf.common_reports.denovo_report.EffectCell property)
numeric (gpf.pheno.prepare.measure_classifier.Convertible attribute)
O
oauth_cookie_to_header() (in module utils.authentication)
observed_rate_per_child (gpf.common_reports.denovo_report.EffectCell property)
OffsetLayoutDrawer (class in gpf.pedigrees.drawing)
omission (gpf.variants.attributes.Inheritance attribute)
open() (gpf.variants_loaders.vcf.serializer.VcfSerializer method)
open_file() (in module gpf.pheno.pheno_import)
operations (datasets_api.migrations.0001_initial.Migration attribute)
(datasets_api.migrations.0002_dataset_groups.Migration attribute)
(datasets_api.migrations.0003_alter_dataset_options.Migration attribute)
(datasets_api.migrations.0004_dataset_broken.Migration attribute)
(datasets_api.migrations.0005_dataset_dataset_name.Migration attribute)
(datasets_api.migrations.0006_datasethierarchy.Migration attribute)
(datasets_api.migrations.0007_datasethierarchy_direct.Migration attribute)
(datasets_api.migrations.0008_datasethierarchy_instance_id.Migration attribute)
(query_state_save.migrations.0001_initial.Migration attribute)
(query_state_save.migrations.0002_auto_20190205_0736.Migration attribute)
(query_state_save.migrations.0003_querystate_origin_querystate_timestamp.Migration attribute)
(user_queries.migrations.0001_initial.Migration attribute)
(users_api.migrations.0001_initial.Migration attribute)
(users_api.migrations.0002_auto_20190424_0751.Migration attribute)
(users_api.migrations.0003_authenticationlog.Migration attribute)
(users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more.Migration attribute)
(users_api.migrations.0005_gpuserstate.Migration attribute)
OPTION (gpf.variants_loaders.raw.loader.ArgumentType attribute)
or_() (gpf.query_variants.attribute_queries.AttributeQueryTransformerFunction method)
(gpf.query_variants.attribute_queries.AttributeQueryTransformerSQL method)
(gpf.query_variants.attribute_queries.QueryCompoundAdditionTransformer method)
ordinal (gpf.pheno.common.InferenceConfig attribute)
(gpf.pheno.common.MeasureType attribute)
other (gpf.pheno.common.MeasureType attribute)
(gpf.variants.attributes.Inheritance attribute)
other_parent() (gpf.pedigrees.pedigrees.MatingUnit method)
overlap_enrichment_result_dict() (in module gpf.enrichment_tool.event_counters)
overlap_event_counts() (in module gpf.enrichment_tool.event_counters)
P
PAGE_SIZE (gpf.gene_profile.db.GeneProfileDB attribute)
(gpf.pheno.browser.PhenoBrowser attribute)
page_size_query_param (utils.pagination.WdaePageNumberPagination attribute)
paginate_queryset() (utils.pagination.WdaePageNumberPagination method)
parent (gpf.variants.attributes.Role attribute)
parents (gpf.studies.study.GenotypeData property)
(studies.study_wrapper.WDAEAbstractStudy property)
parents_id() (gpf.pedigrees.family_role_builder.Mating static method)
parents_zygosity (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute)
ParquetGenotypeStorage (class in gpf.parquet_storage.storage)
ParquetImportStorage (class in gpf.parquet_storage.storage)
ParquetLoader (class in gpf.parquet.schema2.loader)
(class in gpf.variants_loaders.parquet.loader)
ParquetLoaderException
ParquetLoaderVariants (class in gpf.parquet_storage.storage)
parse() (gpf.parquet.partition_descriptor.PartitionDescriptor static method)
(sentry.views.PlainTextParser method)
parse_and_interpolate() (gpf.configuration.gpf_config_parser.GPFConfigParser static method)
parse_and_interpolate_file() (gpf.configuration.gpf_config_parser.GPFConfigParser class method)
parse_cli_argument() (gpf.variants_loaders.raw.loader.CLIArgument method)
parse_cli_arguments() (gpf.pedigrees.loader.FamiliesLoader class method)
(gpf.variants_loaders.cnv.loader.CNVLoader class method)
(gpf.variants_loaders.dae.loader.DaeTransmittedLoader class method)
(gpf.variants_loaders.dae.loader.DenovoLoader class method)
(gpf.variants_loaders.raw.loader.CLILoader class method)
(gpf.variants_loaders.vcf.loader.VcfLoader class method)
(in module gpf.tools.dae2vcf)
(in module gpf.tools.denovo2vcf)
(in module gpf.tools.vcf2tsv)
parse_denovo_gene_sets_config() (in module gpf.gene_sets.denovo_gene_sets_config)
parse_denovo_gene_sets_study_config() (in module gpf.gene_sets.denovo_gene_sets_config)
parse_dgsc_query() (in module gpf.gene_sets.denovo_gene_sets_config)
parse_dict() (gpf.parquet.partition_descriptor.PartitionDescriptor static method)
parse_duckdb_config() (in module gpf.duckdb_storage.duckdb_storage_config)
parse_person_set_collection_config() (in module gpf.person_sets)
(in module gpf.person_sets.person_sets)
parse_person_set_collections_study_config() (in module gpf.person_sets)
(in module gpf.person_sets.person_sets)
parse_person_set_config() (in module gpf.person_sets)
(in module gpf.person_sets.person_sets)
parse_query_params() (in module utils.query_params)
parse_recurrency_criteria() (in module gpf.gene_sets.denovo_gene_sets_config)
parse_string() (gpf.parquet.partition_descriptor.PartitionDescriptor static method)
Partition (class in gpf.parquet.partition_descriptor)
partition_directory() (gpf.parquet.partition_descriptor.PartitionDescriptor static method)
partition_filename() (gpf.parquet.partition_descriptor.PartitionDescriptor static method)
PartitionDescriptor (class in gpf.parquet.partition_descriptor)
PASSED (gpf.tools.gpf_validation_runner.TestStatus attribute)
passed_case_count (gpf.tools.gpf_validation_runner.AbstractRunner property)
(gpf.tools.gpf_validation_runner.MainRunner property)
paternal_aunt (gpf.variants.attributes.Role attribute)
paternal_cousin (gpf.variants.attributes.Role attribute)
paternal_grandfather (gpf.variants.attributes.Role attribute)
paternal_grandmother (gpf.variants.attributes.Role attribute)
paternal_half_sibling (gpf.variants.attributes.Role attribute)
paternal_uncle (gpf.variants.attributes.Role attribute)
path (gpf.pheno.common.DataDictionaryConfig attribute)
(gpf.pheno.common.GPFInstanceConfig attribute)
(gpf.pheno.common.InstrumentConfig attribute)
(gpf.pheno.common.InstrumentDictionaryConfig attribute)
path_to_partitions() (gpf.parquet.partition_descriptor.PartitionDescriptor static method)
PDFLayoutDrawer (class in gpf.pedigrees.drawing)
ped_1() (in module enrichment_api.tests.test_t4c8_enrichment)
ped_df (gpf.pedigrees.families_data.FamiliesData property)
pedigree (gpf.pheno.common.PhenoImportConfig attribute)
(gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute)
(gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute)
(gpf.testing.import_helpers.StudyInputLayout attribute)
pedigree_import() (in module gpf.testing.import_helpers)
pedigree_parquet_schema() (in module gpf.parquet.parquet_writer)
pedigree_samples() (gpf.pedigrees.families_data.FamiliesData method)
PeopleCounter (class in gpf.common_reports.people_counter)
PeopleCounters (class in gpf.common_reports.people_counter)
PeopleReport (class in gpf.common_reports.people_counter)
percent_of_children_with_events (gpf.common_reports.denovo_report.EffectCell property)
Person (class in gpf.pedigrees.family)
person_column (gpf.pheno.common.InstrumentConfig attribute)
(gpf.pheno.common.PhenoImportConfig attribute)
(gpf.pheno.pheno_import.ImportInstrument attribute)
person_ids (gpf.studies.study.PSCQueryAdjustments attribute)
person_ids() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
person_set_collections (gpf.pheno.common.StudyConfig attribute)
(gpf.pheno.pheno_data.PhenotypeData property)
(gpf.pheno.pheno_data.PhenotypeGroup property)
(gpf.pheno.pheno_data.PhenotypeStudy property)
(gpf.studies.study.GenotypeData property)
(studies.study_wrapper.WDAEAbstractStudy property)
person_sets_api
module
person_sets_api.tests
module
person_sets_api.tests.test_person_sets_api
module
PersonFilter (class in gpf.person_filters)
(class in gpf.person_filters.person_filters)
PersonFilterRange (class in gpf.person_filters)
(class in gpf.person_filters.person_filters)
PersonFilterSet (class in gpf.person_filters)
(class in gpf.person_filters.person_filters)
persons (gpf.enrichment_tool.genotype_helper.AlleleEvent attribute)
persons_with_parent() (gpf.pedigrees.families_data.FamiliesData method)
persons_with_parents() (gpf.pedigrees.families_data.FamiliesData method)
persons_without_parents() (gpf.pedigrees.families_data.FamiliesData method)
PersonSet (class in gpf.person_sets)
(class in gpf.person_sets.person_sets)
PersonSetCollection (class in gpf.person_sets)
(class in gpf.person_sets.person_sets)
PersonSetCollectionConfig (class in gpf.person_sets)
(class in gpf.person_sets.person_sets)
PersonSetConfig (class in gpf.person_sets)
(class in gpf.person_sets.person_sets)
pheno_browser_api
module
pheno_browser_api.pheno_browser_helper
module
pheno_browser_api.tests
module
pheno_cli_parser() (in module gpf.pheno.build_pheno_browser)
(in module gpf.pheno.import_tools)
(in module gpf.pheno.pheno_import)
(in module gpf.pheno.update_pheno_descriptions)
pheno_id (gpf.pheno.pheno_data.PhenotypeData property)
pheno_tool_api
module
pheno_tool_api.adapter
module
pheno_tool_api.tests
module
pheno_tool_api.tests.test_pheno_tool_api
module
PhenoBrowser (class in gpf.pheno.browser)
PhenoBrowserHelper (class in pheno_browser_api.pheno_browser_helper)
PhenoDb (class in gpf.pheno.db)
PhenoFilter (class in gpf.person_filters)
(class in gpf.person_filters.person_filters)
PhenoFilterRange (class in gpf.person_filters)
(class in gpf.person_filters.person_filters)
PhenoFilterSet (class in gpf.person_filters)
(class in gpf.person_filters.person_filters)
PhenoImportConfig (class in gpf.pheno.common)
PhenoRegistry (class in gpf.pheno.registry)
PhenoResult (class in gpf.pheno_tool.tool)
PhenoTool (class in gpf.pheno_tool.tool)
PhenoToolAdapter (class in gpf.pheno_tool.pheno_tool_adapter)
(class in pheno_tool_api.adapter)
PhenoToolAdapterBase (class in gpf.pheno_tool.pheno_tool_adapter)
(class in pheno_tool_api.adapter)
PhenoToolHelper (class in gpf.pheno_tool.tool)
phenotype (gpf.studies.study.GenotypeData property)
PHENOTYPE_ATTRS (studies.response_transformer.ResponseTransformer attribute)
phenotype_data (studies.study_wrapper.WDAEAbstractStudy property)
phenotype_person_sets() (in module studies.tests.test_response_transformer_columns)
phenotype_storages (gpf.gpf_instance.gpf_instance.GPFInstance property)
(gpf.gpf_instance.GPFInstance property)
PhenotypeData (class in gpf.pheno.pheno_data)
PhenotypeGroup (class in gpf.pheno.pheno_data)
PhenotypeStorage (class in gpf.pheno.storage)
PhenotypeStorageRegistry (class in gpf.pheno.storage)
PhenotypeStudy (class in gpf.pheno.pheno_data)
PlainTextParser (class in sentry.views)
Point (class in gpf.pedigrees.layout)
poisson_test() (in module gpf.enrichment_tool.samocha_background)
position (gpf.variants.core.Allele property)
(gpf.variants.core.Allele.Type attribute)
(gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
(gpf.variants.variant.SummaryVariant property)
possible_denovo (gpf.variants.attributes.Inheritance attribute)
possible_omission (gpf.variants.attributes.Inheritance attribute)
prb (gpf.variants.attributes.Role attribute)
PreparePhenoBrowserBase (class in gpf.pheno.prepare_data)
preview_sources() (in module genotype_browser.tests.conftest)
process_config() (gpf.configuration.gpf_config_parser.GPFConfigParser static method)
process_config_raw() (gpf.configuration.gpf_config_parser.GPFConfigParser static method)
process_parquet() (in module gpf.parquet.schema2.annotate_schema2_parquet)
process_region() (in module gpf.gene_profile.generate_gene_profile)
produce_download() (pheno_tool_api.adapter.PhenoToolAdapter method)
(pheno_tool_api.adapter.PhenoToolAdapterBase method)
produce_genotype() (gpf.variants_loaders.dae.loader.DenovoLoader static method)
produce_regions() (in module gpf.parquet.schema2.annotate_schema2_parquet)
produce_schema2_annotation_tasks() (in module gpf.parquet.schema2.annotate_schema2_parquet)
produce_schema2_merging_tasks() (in module gpf.parquet.schema2.annotate_schema2_parquet)
psc_config() (in module enrichment_api.tests.conftest)
psc_id (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute)
(gpf.person_sets.person_sets.PSCQuery attribute)
(gpf.person_sets.PSCQuery attribute)
PSCQuery (class in gpf.person_sets)
(class in gpf.person_sets.person_sets)
PSCQueryAdjustments (class in gpf.studies.study)
pseudo_autosomal (gpf.variants.attributes.GeneticModel attribute)
pub_med (gpf.studies.study.GenotypeData property)
put_value_in_result_queue() (gpf.query_variants.query_runners.QueryRunner method)
pvalues (gpf.pheno.utils.lin_regress.LinearRegression property)
Q
QUAD (gpf.pedigrees.family.FamilyTag attribute)
query_base
module
query_fpids() (gpf.person_sets.person_sets.PersonSetCollection method)
(gpf.person_sets.PersonSetCollection method)
query_gp_statistics() (gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
query_gps() (gpf.gene_profile.db.GeneProfileDB method)
query_load() (in module query_state_save.tests.conftest)
query_person_ids() (gpf.person_sets.person_sets.PersonSetCollection method)
(gpf.person_sets.PersonSetCollection method)
query_save() (in module query_state_save.tests.conftest)
query_state_save
module
query_state_save.migrations
module
query_state_save.migrations.0001_initial
module
query_state_save.migrations.0002_auto_20190205_0736
module
query_state_save.migrations.0003_querystate_origin_querystate_timestamp
module
query_state_save.tests
module
query_state_save.tests.conftest
module
query_summary_variants() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method)
(gpf.parquet_storage.storage.ParquetLoaderVariants method)
(gpf.studies.study.GenotypeData method)
query_transformer() (in module studies.tests.test_study_group_person_sets_queries)
(in module studies.tests.test_study_wrapper_person_sets)
(in module studies.tests.test_study_wrapper_unique_variants_query)
query_variants() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method)
(gpf.parquet_storage.storage.ParquetLoaderVariants method)
(gpf.studies.study.GenotypeData method)
query_variants_download_wdae() (studies.study_wrapper.WDAEAbstractStudy method)
(studies.study_wrapper.WDAEStudy method)
query_variants_preview_wdae() (studies.study_wrapper.WDAEAbstractStudy method)
(studies.study_wrapper.WDAEStudy method)
query_variants_raw() (studies.study_wrapper.WDAEStudy method)
query_variants_wdae() (studies.study_wrapper.WDAEAbstractStudy method)
(studies.study_wrapper.WDAEStudy method)
QueryBuilderBase (class in gpf.query_variants.sql.schema2.sql_query_builder)
QueryCompoundAdditionTransformer (class in gpf.query_variants.attribute_queries)
QueryHeuristics (class in gpf.query_variants.sql.schema2.sql_query_builder)
QueryResult (class in gpf.query_variants.query_runners)
QueryRunner (class in gpf.query_variants.query_runners)
QueryTransformer (class in studies.query_transformer)
QueryTransformerProtocol (class in studies.study_wrapper)
QueryVariants (class in gpf.query_variants.base_query_variants)
QueryVariantsBase (class in gpf.query_variants.base_query_variants)
QUOTE (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute)
R
RankRange (class in gpf.pheno.common)
raw (gpf.pheno.common.MeasureType attribute)
RawFamilyVariants (class in gpf.inmemory_storage.raw_variants)
RawMemoryVariants (class in gpf.inmemory_storage.raw_variants)
RawVariantsQueryRunner (class in gpf.inmemory_storage.raw_variants)
read_and_classify_measure() (in module gpf.pheno.pheno_import)
read_instrument_measure_names() (in module gpf.pheno.pheno_import)
read_only (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute)
(gpf.genotype_storage.genotype_storage.GenotypeStorage property)
read_pedigree() (in module gpf.pheno.pheno_import)
Reader (class in gpf.parquet.schema2.loader)
ReadOnlyDBAuthentication (class in utils.authentication)
ready() (gpf_instance.apps.WDAEConfig method)
real_attr() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
real_persons (gpf.pedigrees.families_data.FamiliesData property)
Realization (class in gpf.pedigrees.pedigrees)
ReannotateInstanceTool (class in gpf.tools.reannotate_instance)
rebuild_families() (gpf.studies.study.GenotypeDataGroup method)
rec (gpf.enrichment_tool.event_counters.EnrichmentResult attribute)
(gpf.enrichment_tool.event_counters.EventCountersResult attribute)
(gpf.enrichment_tool.event_counters.EventsResult attribute)
(gpf.enrichment_tool.event_counters.VariantEventsResult attribute)
rec_genes (gpf.enrichment_tool.event_counters.EnrichmentResult attribute)
(gpf.enrichment_tool.event_counters.EventCountersResult attribute)
recurrency (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute)
(gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute)
RecurrentCriteria (class in gpf.gene_sets.denovo_gene_sets_config)
red (gpf_web.default_settings.CustomFormatter attribute)
redefine() (gpf.pedigrees.families_data.FamiliesData method)
(gpf.pedigrees.family.Family method)
(gpf.pedigrees.family.Person method)
ref_allele (gpf.variants.variant.SummaryVariant property)
reference (gpf.variants.attributes.Inheritance attribute)
(gpf.variants.core.Allele property)
(gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
(gpf.variants.variant.SummaryVariant property)
reference_genome (gpf.gpf_instance.gpf_instance.GPFInstance property)
(gpf.gpf_instance.GPFInstance property)
reference_genotype() (in module gpf.utils.variant_utils)
region_bin (gpf.import_tools.import_tools.Bucket attribute)
(gpf.parquet.partition_descriptor.Partition attribute)
region_bins (gpf.query_variants.sql.schema2.sql_query_builder.QueryHeuristics attribute)
region_bins() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
region_bins_count() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
REGION_BINS_HEURISTIC_CUTOFF (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase attribute)
region_to_region_bins() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
regions (gpf.import_tools.import_tools.Bucket attribute)
regions() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
register_default_storage() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method)
(gpf.pheno.storage.PhenotypeStorageRegistry method)
register_genotype_data() (gpf.studies.variants_db.VariantsDb method)
register_genotype_storage() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method)
register_genotype_storage_factory() (in module gpf.genotype_storage.genotype_storage_registry)
register_import_storage_factory() (in module gpf.import_tools.import_tools)
register_phenotype_data() (gpf.pheno.registry.PhenoRegistry method)
register_phenotype_storage() (gpf.pheno.storage.PhenotypeStorageRegistry method)
register_storage_config() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method)
(gpf.pheno.storage.PhenotypeStorageRegistry method)
register_storages_configs() (gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method)
(gpf.pheno.storage.PhenotypeStorageRegistry method)
regression_display_names (gpf.pheno.browser.PhenoBrowser property)
regression_display_names_with_ids (gpf.pheno.browser.PhenoBrowser property)
regression_ids (gpf.pheno.browser.PhenoBrowser property)
RegressionMeasure (class in gpf.pheno.common)
regressions (gpf.pheno.common.StudyConfig attribute)
reload() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method)
(gpf.gpf_instance.gpf_instance.GPFInstance method)
(gpf.gpf_instance.GPFInstance method)
(gpf.studies.variants_db.VariantsDb method)
remove_annoying_characters() (in module gpf.pheno.utils.commons)
remove_elements() (gpf.common_reports.denovo_report.EffectRow method)
remove_empty_person_sets() (gpf.person_sets.person_sets.PersonSetCollection static method)
(gpf.person_sets.PersonSetCollection static method)
remove_none_values() (in module studies.study_wrapper)
remove_study_config() (gpf.tools.dataset_helpers.DatasetHelpers method)
rename_study_config() (gpf.tools.dataset_helpers.DatasetHelpers method)
replace_tables() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method)
report_variant() (gpf.tools.liftover_tools.VCFLiftoverTool static method)
report_vcf_variant() (gpf.tools.liftover_tools.VCFLiftoverTool static method)
request_logging() (in module utils.logger)
request_logging_function_view() (in module utils.logger)
reset (gpf_web.default_settings.CustomFormatter attribute)
reset_regions() (gpf.variants_loaders.raw.loader.VariantsGenotypesLoader method)
(gpf.variants_loaders.raw.loader.VariantsLoader method)
(gpf.variants_loaders.vcf.loader.VcfLoader method)
resolve_tags() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
resource_id (gpf.enrichment_tool.base_enrichment_background.BaseEnrichmentBackground property)
(gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property)
(gpf.enrichment_tool.resource_implementations.enrichment_resource_impl.EnrichmentBackgroundResourceImplementation property)
(gpf.genomic_scores.scores.ScoreDesc attribute)
response_transformer() (in module studies.tests.test_study_group_person_sets_queries)
ResponseTransformer (class in studies.response_transformer)
ResponseTransformerProtocol (class in studies.study_wrapper)
result_queue (gpf.query_variants.query_runners.QueryRunner property)
Role (class in gpf.variants.attributes)
role (gpf.pedigrees.family.Person property)
role_labels() (in module gpf.pheno.graphs)
roles (gpf.studies.study.PSCQueryAdjustments attribute)
roles() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
rules (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute)
run() (gpf.duckdb_storage.duckdb2_variants.DuckDb2Runner method)
(gpf.duckdb_storage.duckdb_variants.DuckDbRunner method)
(gpf.inmemory_storage.raw_variants.RawVariantsQueryRunner method)
(gpf.pheno.prepare_data.PreparePhenoBrowserBase method)
(gpf.query_variants.query_runners.QueryRunner method)
(gpf.tools.gpf_validation_runner.GenotypeBrowserRunner method)
(gpf.tools.liftover_tools.LiftoverTool method)
(gpf.tools.reannotate_instance.ReannotateInstanceTool method)
run_with_project() (in module gpf.import_tools.cli)
RUNNER_CLASS (gpf.duckdb_storage.duckdb_variants.DuckDbVariants attribute)
(gpf.query_variants.base_query_variants.QueryVariantsBase attribute)
(gpf.query_variants.sql.schema2.base_variants.SqlSchema2Variants attribute)
S
safe_db_name() (in module gpf.pheno.db)
samocha_background() (in module enrichment_api.tests.conftest)
SamochaEnrichmentBackground (class in gpf.enrichment_tool.samocha_background)
sample_index (gpf.pedigrees.family.Person property)
samples_index (gpf.pedigrees.family.Family property)
SandwichInstance (class in gpf.pedigrees.pedigrees)
SandwichSolver (class in gpf.pedigrees.pedigrees)
save() (gpf.common_reports.common_report.CommonReport method)
(gpf.gene_sets.denovo_gene_set_collection.DenovoGeneSetCollection method)
(gpf.pheno.browser.PhenoBrowser method)
save_descriptions() (gpf.pheno.browser.PhenoBrowser method)
(gpf.pheno.db.PhenoDb method)
(in module gpf.pheno.update_pheno_descriptions)
save_families() (gpf.pedigrees.loader.FamiliesLoader static method)
save_fig() (gpf.pheno.prepare_data.PreparePhenoBrowserBase class method)
save_object() (in module query_state_save.tests.conftest)
save_ped_df_to_parquet() (in module gpf.parquet.parquet_writer)
save_pedigree() (gpf.pedigrees.loader.FamiliesLoader static method)
save_regression() (gpf.pheno.browser.PhenoBrowser method)
save_regression_values() (gpf.pheno.browser.PhenoBrowser method)
save_study_config() (in module gpf.import_tools.import_tools)
scale() (gpf.pedigrees.layout.Layout method)
schema() (gpf.parquet.schema2.serializers.AlleleParquetSerializer method)
(gpf.parquet.schema2.serializers.FamilyAlleleParquetSerializer method)
(gpf.parquet.schema2.serializers.SummaryAlleleParquetSerializer method)
schema1_partition() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
schema2_project_dataset_layout() (in module gpf.schema2_storage.schema2_import_storage)
Schema2DatasetLayout (class in gpf.schema2_storage.schema2_layout)
Schema2ImportStorage (class in gpf.schema2_storage.schema2_import_storage)
Schema2SummaryVariantBatchConsumer (class in gpf.parquet.schema2.variants_parquet_writer)
Schema2SummaryVariantConsumer (class in gpf.parquet.schema2.variants_parquet_writer)
Schema2SummaryVariantsBatchSource (class in gpf.parquet.schema2.processing_pipeline)
Schema2SummaryVariantsSource (class in gpf.parquet.schema2.processing_pipeline)
Schema2VariantBatchConsumer (class in gpf.parquet.schema2.variants_parquet_writer)
Schema2VariantConsumer (class in gpf.parquet.schema2.variants_parquet_writer)
score_id (gpf.enrichment_tool.gene_weights_background.GeneScoreEnrichmentBackground property)
ScoreDesc (class in gpf.genomic_scores.scores)
search_measures() (gpf.pheno.browser.PhenoBrowser method)
(gpf.pheno.pheno_data.PhenotypeData method)
(pheno_browser_api.pheno_browser_helper.BasePhenoBrowserHelper method)
(pheno_browser_api.pheno_browser_helper.PhenoBrowserHelper method)
select_events_in_person_set() (gpf.enrichment_tool.event_counters.CounterBase method)
selected_family_tags (gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute)
selected_person_set_collections (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute)
selected_person_sets (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute)
(gpf.person_sets.person_sets.PSCQuery attribute)
(gpf.person_sets.PSCQuery attribute)
sentry
module
sentry() (in module sentry.views)
sentry.tests
module
sentry.tests.test_sentry
module
sentry.urls
module
sentry.views
module
serialize() (enrichment_api.enrichment_serializer.EnrichmentSerializer method)
(gpf.parquet.partition_descriptor.PartitionDescriptor method)
(gpf.variants_loaders.vcf.serializer.VcfSerializer method)
serialize_all() (enrichment_api.enrichment_serializer.EnrichmentSerializer method)
serialize_common_filter() (enrichment_api.enrichment_serializer.EnrichmentSerializer method)
serialize_enrichment_result() (enrichment_api.enrichment_serializer.EnrichmentSerializer method)
serialize_family() (gpf.parquet.schema2.serializers.JsonVariantsDataSerializer method)
(gpf.parquet.schema2.serializers.VariantsDataSerializer method)
serialize_female() (enrichment_api.enrichment_serializer.EnrichmentSerializer method)
serialize_full_variant() (gpf.variants_loaders.vcf.serializer.VcfSerializer method)
serialize_male() (enrichment_api.enrichment_serializer.EnrichmentSerializer method)
serialize_overlap_filter() (enrichment_api.enrichment_serializer.EnrichmentSerializer method)
serialize_people_groups() (enrichment_api.enrichment_serializer.EnrichmentSerializer method)
serialize_rec() (enrichment_api.enrichment_serializer.EnrichmentSerializer method)
serialize_rec_filter() (enrichment_api.enrichment_serializer.EnrichmentSerializer method)
serialize_summary() (gpf.parquet.schema2.serializers.JsonVariantsDataSerializer method)
(gpf.parquet.schema2.serializers.VariantsDataSerializer method)
serialize_summary_schema() (in module gpf.parquet.parquet_writer)
SessionAuthenticationWithoutCSRF (class in utils.authentication)
SessionAuthenticationWithUnauthenticatedCSRF (class in utils.authentication)
set_attr() (gpf.pedigrees.family.Person method)
(in module gpf.pedigrees.family_tag_builder)
set_attribute() (gpf.variants_loaders.raw.loader.VariantsLoader method)
set_figure_size() (in module gpf.pheno.graphs)
set_fit_request() (gpf.pheno.utils.lin_regress.LinearRegression method)
set_matched_alleles() (gpf.variants.variant.SummaryVariant method)
set_negative_stats() (gpf.pheno_tool.tool.PhenoResult method)
set_positive_stats() (gpf.pheno_tool.tool.PhenoResult method)
set_result_queue() (gpf.query_variants.query_runners.QueryRunner method)
set_score_request() (gpf.pheno.utils.lin_regress.LinearRegression method)
set_study_id() (gpf.query_variants.query_runners.QueryRunner method)
set_tag() (gpf.pedigrees.family.Family method)
(gpf.pedigrees.family.Person method)
(in module gpf.pedigrees.family_tag_builder)
setup() (gpf_instance.extension.GPFExtensionBase method)
setup_dataset() (in module gpf.testing.import_helpers)
setup_dataset_config() (in module gpf.testing.import_helpers)
setup_gpf_instance() (in module gpf.testing.setup_helpers)
setup_import_project() (in module gpf.testing.import_helpers)
setup_import_project_config() (in module gpf.testing.import_helpers)
setup_t4c8_grr() (in module utils.testing)
setup_t4c8_instance() (in module gpf.utils.testing)
(in module utils.testing)
setup_wgpf_instance() (in module utils.testing)
Sex (class in gpf.variants.attributes)
sex (gpf.gene_sets.denovo_gene_sets_config.DGSCQuery attribute)
(gpf.pedigrees.family.Person property)
sex_zygosity (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute)
sexes (gpf.gene_sets.denovo_gene_sets_config.DenovoGeneSetsConfig attribute)
(gpf.gene_sets.denovo_gene_sets_config.SexesCriteria attribute)
(gpf.studies.study.PSCQueryAdjustments attribute)
sexes() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
SexesCriteria (class in gpf.gene_sets.denovo_gene_sets_config)
short() (gpf.variants.attributes.Sex method)
(gpf.variants.attributes.Status method)
shutdown() (gpf.duckdb_storage.duckdb_genotype_storage.AbstractDuckDbStorage method)
(gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method)
(gpf.genotype_storage.genotype_storage.GenotypeStorage method)
(gpf.genotype_storage.genotype_storage_registry.GenotypeStorageRegistry method)
(gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method)
(gpf.parquet_storage.storage.ParquetGenotypeStorage method)
(gpf.pheno.registry.PhenoRegistry method)
(gpf.pheno.storage.PhenotypeStorage method)
(gpf.pheno.storage.PhenotypeStorageRegistry method)
sib (gpf.variants.attributes.Role attribute)
SibshipUnit (class in gpf.pedigrees.pedigrees)
simple_query_data() (in module query_state_save.tests.conftest)
SIMPLEX (gpf.pedigrees.family.FamilyTag attribute)
SingleCriteria (class in gpf.gene_sets.denovo_gene_sets_config)
SingleVcfLoader (class in gpf.variants_loaders.vcf.loader)
SIZE (gpf.pedigrees.layout.IndividualWithCoordinates attribute)
size() (gpf.parquet.schema2.parquet_io.ContinuousParquetFileWriter method)
(gpf.parquet.schema2.variants_parquet_writer.ContinuousParquetFileWriter method)
skip (gpf.pheno.common.InferenceConfig attribute)
skip_pedigree_measures (gpf.pheno.common.PhenoImportConfig attribute)
skipped (gpf.pheno.common.MeasureType attribute)
small_deletion (gpf.variants.core.Allele.Type attribute)
SMALL_DPI (gpf.pheno.prepare_data.PreparePhenoBrowserBase attribute)
small_insertion (gpf.variants.core.Allele.Type attribute)
small_values_desc (gpf.genomic_scores.scores.ScoreDesc attribute)
solve() (gpf.pedigrees.pedigrees.SandwichSolver static method)
source (gpf.genomic_scores.scores.ScoreDesc attribute)
(gpf.person_sets.person_sets.SourceConfig attribute)
(gpf.person_sets.SourceConfig attribute)
SourceConfig (class in gpf.person_sets)
(class in gpf.person_sets.person_sets)
sources (gpf.person_sets.person_sets.PersonSetCollectionConfig attribute)
(gpf.person_sets.PersonSetCollectionConfig attribute)
SPECIAL_ATTRS (studies.response_transformer.ResponseTransformer attribute)
split_events() (gpf.enrichment_tool.event_counters.CounterBase method)
split_heuristics() (gpf.query_variants.sql.schema2.sql_query_builder.QueryBuilderBase method)
split_location() (gpf.variants_loaders.dae.loader.DenovoLoader static method)
spouse (gpf.variants.attributes.Role attribute)
SqlQueryBuilder (class in gpf.query_variants.sql.schema2.sql_query_builder)
SqlSchema2Variants (class in gpf.query_variants.sql.schema2.base_variants)
start (gpf.gene_sets.denovo_gene_sets_config.RecurrentCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.SingleCriteria attribute)
(gpf.gene_sets.denovo_gene_sets_config.TripleCriteria attribute)
start() (gpf.duckdb_storage.duckdb_genotype_storage.DuckDbParquetStorage method)
(gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3ParquetStorage method)
(gpf.duckdb_storage.duckdb_genotype_storage.DuckDbS3Storage method)
(gpf.duckdb_storage.duckdb_genotype_storage.DuckDbStorage method)
(gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage method)
(gpf.genotype_storage.genotype_storage.GenotypeStorage method)
(gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage method)
(gpf.parquet_storage.storage.ParquetGenotypeStorage method)
(gpf.query_variants.query_runners.QueryResult method)
(gpf.query_variants.query_runners.QueryRunner method)
Status (class in gpf.variants.attributes)
status (gpf.pedigrees.family.Person property)
status_zygosity (gpf.query_variants.sql.schema2.sql_query_builder.ZygosityQuery attribute)
statuses() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
step_dad (gpf.variants.attributes.Role attribute)
step_mom (gpf.variants.attributes.Role attribute)
storage_dir (gpf.pheno.common.DestinationConfig attribute)
storage_id (gpf.pheno.common.DestinationConfig attribute)
storage_type (gpf.duckdb_storage.duckdb_storage_config.DuckDbConf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbParquetConf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute)
store_junit_results() (gpf.tools.gpf_validation_runner.MainRunner static method)
store_results() (gpf.tools.gpf_validation_runner.GenotypeBrowserRunner method)
(gpf.tools.gpf_validation_runner.MainRunner method)
str2fgt() (in module gpf.utils.variant_utils)
str2gt() (in module gpf.utils.variant_utils)
str2lists() (in module gpf.utils.variant_utils)
str2mat() (in module gpf.utils.variant_utils)
str2mat_adjust_colsep() (in module gpf.utils.variant_utils)
STREAMING_CHUNK_SIZE (studies.response_transformer.ResponseTransformer attribute)
string_type() (gpf.query_variants.sql.schema2.base_query_builder.Dialect static method)
studies
module
studies.conftest
module
studies.query_transformer
module
studies.response_transformer
module
studies.study_wrapper
module
studies.tests
module
studies.tests.test_pheno_measures_columns
module
studies.tests.test_query_transformer
module
studies.tests.test_query_transformer_family_tags
module
studies.tests.test_query_transformer_present_in_child_and_parent
module
studies.tests.test_response_transformer_columns
module
studies.tests.test_study_config_genotype_browser_columns
module
studies.tests.test_study_group_person_sets_queries
module
studies.tests.test_study_query_request
module
studies.tests.test_study_wrapper
module
studies.tests.test_study_wrapper_person_sets
module
studies.tests.test_study_wrapper_queries
module
studies.tests.test_study_wrapper_unique_variants_query
module
study (gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute)
(gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute)
study_1() (in module enrichment_api.tests.test_t4c8_enrichment)
(in module studies.tests.test_study_group_person_sets_queries)
study_2() (in module studies.tests.test_study_group_person_sets_queries)
study_config (gpf.pheno.common.PhenoImportConfig attribute)
study_configs (gpf.genotype_storage.genotype_storage.GenotypeStorage property)
study_data() (in module enrichment_api.tests.conftest)
study_id (gpf.import_tools.import_tools.ImportProject property)
(gpf.studies.study.GenotypeData property)
(gpf.testing.import_helpers.StudyInputLayout attribute)
(studies.study_wrapper.WDAEAbstractStudy property)
study_phenotype (gpf.studies.study.GenotypeDataStudy property)
study_type (gpf.studies.study.GenotypeData property)
study_update() (in module gpf.testing.import_helpers)
StudyConfig (class in gpf.pheno.common)
StudyConfigBuilder (class in gpf.configuration.study_config_builder)
StudyConfigsAdjustmentCommand (class in gpf.gpf_instance.adjustments.gpf_instance_adjustments)
StudyInputLayout (class in gpf.testing.import_helpers)
substitution (gpf.variants.core.Allele.Type attribute)
summary (gpf.query_variants.sql.schema2.sql_query_builder.Db2Layout attribute)
(gpf.schema2_storage.schema2_layout.Schema2DatasetLayout attribute)
summary() (gpf.tools.gpf_validation_runner.MainRunner method)
summary_allele (gpf.variants.family_variant.FamilyAllele attribute)
summary_allele_from_record() (gpf.variants.variant.SummaryVariantFactory static method)
summary_attributes (gpf.variants.family_variant.FamilyAllele property)
summary_base() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
SUMMARY_COLUMNS (gpf.parquet.schema2.loader.ParquetLoader attribute)
summary_download_sources() (in module genotype_browser.tests.conftest)
summary_index (gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
(gpf.variants.variant.SummaryAllele property)
(gpf.variants.variant.SummaryVariant property)
summary_partition() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
summary_partition_schema() (gpf.parquet.partition_descriptor.PartitionDescriptor method)
summary_preview_sources() (in module genotype_browser.tests.conftest)
summary_query() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method)
summary_variant (gpf.variants_loaders.raw.loader.FullVariant attribute)
summary_variant_filter_function() (gpf.inmemory_storage.raw_variants.RawFamilyVariants class method)
summary_variant_from_records() (gpf.variants.variant.SummaryVariantFactory static method)
summary_variant_from_vcf() (gpf.variants.variant.SummaryVariantFactory static method)
summary_variants() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder method)
summary_variants_iterator() (gpf.inmemory_storage.raw_variants.RawFamilyVariants method)
SummaryAllele (class in gpf.variants.variant)
SummaryAlleleParquetSerializer (class in gpf.parquet.schema2.serializers)
SummaryQueryBuilder (class in gpf.query_variants.sql.schema2.summary_builder)
SummaryVariant (class in gpf.variants.variant)
SummaryVariantFactory (class in gpf.variants.variant)
svuid (gpf.variants.variant.SummaryVariant property)
symlink_pedigree_and_family_variants() (in module gpf.parquet.schema2.annotate_schema2_parquet)
SyntaxSugarTransformer (class in gpf.query_variants.attribute_queries)
T
t4c8_fixture() (in module enrichment_api.tests.conftest)
t4c8_gpf() (in module gpf.testing.t4c8_import)
tag_affected_dad_family() (in module gpf.pedigrees.family_tag_builder)
tag_affected_mom_family() (in module gpf.pedigrees.family_tag_builder)
tag_affected_prb_family() (in module gpf.pedigrees.family_tag_builder)
tag_affected_sib_family() (in module gpf.pedigrees.family_tag_builder)
tag_control_family() (in module gpf.pedigrees.family_tag_builder)
tag_families_data() (in module gpf.pedigrees.families_data)
tag_family() (gpf.pedigrees.family_tag_builder.FamilyTagsBuilder method)
tag_family_type() (gpf.pedigrees.family_tag_builder.FamilyTagsBuilder method)
tag_female_prb_family() (in module gpf.pedigrees.family_tag_builder)
tag_labels (gpf.pedigrees.family.Family property)
tag_male_prb_family() (in module gpf.pedigrees.family_tag_builder)
tag_missing_dad_family() (in module gpf.pedigrees.family_tag_builder)
tag_missing_mom_family() (in module gpf.pedigrees.family_tag_builder)
tag_multiplex_family() (in module gpf.pedigrees.family_tag_builder)
tag_nuclear_family() (in module gpf.pedigrees.family_tag_builder)
tag_quad_family() (in module gpf.pedigrees.family_tag_builder)
tag_simplex_family() (in module gpf.pedigrees.family_tag_builder)
tag_trio_family() (in module gpf.pedigrees.family_tag_builder)
tag_unaffected_dad_family() (in module gpf.pedigrees.family_tag_builder)
tag_unaffected_mom_family() (in module gpf.pedigrees.family_tag_builder)
tag_unaffected_prb_family() (in module gpf.pedigrees.family_tag_builder)
tag_unaffected_sib_family() (in module gpf.pedigrees.family_tag_builder)
tags (gpf.pedigrees.family.Family property)
(gpf.pedigrees.family.Person property)
TAGS (gpf.pedigrees.family_tag_builder.FamilyTagsBuilder attribute)
tags_or_mode (gpf.query_variants.sql.schema2.sql_query_builder.TagsQuery attribute)
tags_to_family_ids() (gpf.query_variants.base_query_variants.QueryVariants method)
TagsQuery (class in gpf.query_variants.sql.schema2.sql_query_builder)
tandem_repeat (gpf.variants.core.Allele.Type attribute)
tandem_repeat() (in module gpf.variants.variant)
tandem_repeat_del (gpf.variants.core.Allele.Type attribute)
tandem_repeat_ins (gpf.variants.core.Allele.Type attribute)
test_affected_status() (in module studies.tests.test_query_transformer)
test_attributes_query_roles() (in module studies.tests.test_query_transformer_present_in_child_and_parent)
test_autogenerate_common_report() (in module common_reports_api.tests.test_common_reports_api)
test_bad_gene_score_partition() (in module gene_scores.tests.test_scores_partitions)
test_bad_gene_set_collection_not_found() (in module gene_sets.tests.test_gene_sets_api)
test_build() (in module enrichment_api.tests.test_enrichment_builder)
test_build_people_group_selector() (in module enrichment_api.tests.test_enrichment_builder)
test_build_results() (in module enrichment_api.tests.test_enrichment_builder)
test_build_study_1_enrichment_cache() (in module enrichment_api.tests.test_t4c8_enrichment)
test_collection_configs_view() (in module person_sets_api.tests.test_person_sets_api)
test_collection_domain_view() (in module person_sets_api.tests.test_person_sets_api)
test_configuration() (in module gene_profiles_api.tests.test_agp_api)
(in module gene_profiles_api.tests.test_agp_api_configless)
test_dataset_person_sets_queries() (in module studies.tests.test_study_group_person_sets_queries)
test_dataset_simple() (in module studies.tests.test_study_group_person_sets_queries)
test_default_gene_models_id() (in module genomes_api.tests.test_gene_models_api)
test_denovo_gene_set_download() (in module gene_sets.tests.test_gene_sets_api)
test_denovo_gene_set_not_found() (in module gene_sets.tests.test_gene_sets_api)
test_denovo_gene_sets() (in module gene_sets.tests.test_gene_sets_api)
test_denovo_gene_sets_types() (in module gene_sets.tests.test_gene_sets_api)
test_effect_details_download() (in module genotype_browser.tests.test_effect_types_download)
test_enrichment_api_permissions() (in module enrichment_api.tests.test_enrichment_api)
test_enrichment_models() (in module enrichment_api.tests.test_enrichment_api)
test_enrichment_models_missing_study() (in module enrichment_api.tests.test_enrichment_api)
test_enrichment_test_missing_dataset_id() (in module enrichment_api.tests.test_enrichment_api)
test_enrichment_test_missing_gene_symbols() (in module enrichment_api.tests.test_enrichment_api)
test_enrichment_test_missing_study() (in module enrichment_api.tests.test_enrichment_api)
test_enrichment_test_with_gene_score() (in module enrichment_api.tests.test_enrichment_api)
test_enrichment_test_with_gene_score_with_zero_range() (in module enrichment_api.tests.test_enrichment_api)
test_enrichment_test_with_gene_set() (in module enrichment_api.tests.test_enrichment_api)
test_enrichment_test_with_gene_symbols() (in module enrichment_api.tests.test_enrichment_api)
test_families_data_all_download() (in module common_reports_api.tests.test_common_reports_api)
test_families_data_all_download_no_permissions() (in module common_reports_api.tests.test_common_reports_api)
test_families_data_download() (in module common_reports_api.tests.test_common_reports_api)
test_families_data_download_no_permissions() (in module common_reports_api.tests.test_common_reports_api)
test_families_tags_download() (in module common_reports_api.tests.test_common_reports_api)
test_families_tags_download_errors_on_bad_body() (in module common_reports_api.tests.test_common_reports_api)
test_family_api_permissions() (in module family_api.tests.test_family_api)
test_family_counters() (in module common_reports_api.tests.test_common_reports_api)
test_family_counters_download() (in module common_reports_api.tests.test_common_reports_api)
test_family_details_view() (in module family_api.tests.test_family_api)
test_family_details_view_nonexistent() (in module family_api.tests.test_family_api)
test_full_family_details_view() (in module family_api.tests.test_family_api)
test_full_study_families_view() (in module family_api.tests.test_family_api)
test_gene_score_download() (in module gene_scores.tests.test_gene_scores_views)
test_gene_scores_list_view() (in module gene_scores.tests.test_gene_scores_views)
test_gene_scores_partitions() (in module gene_scores.tests.test_gene_scores_views)
(in module gene_scores.tests.test_scores_partitions)
test_gene_scores_partitions_bad_request() (in module gene_scores.tests.test_gene_scores_views)
test_gene_set_download_missense() (in module gene_sets.tests.test_gene_sets_api)
test_gene_sets_collections() (in module gene_sets.tests.test_gene_sets_api)
test_gene_sets_empty_query() (in module gene_sets.tests.test_gene_sets_api)
test_gene_sets_missing_collection() (in module gene_sets.tests.test_gene_sets_api)
test_gene_view_api_permissions() (in module gene_view.tests.test_gene_view)
test_gene_view_config() (in module gene_view.tests.test_gene_view)
test_gene_view_summary_variants_download() (in module gene_view.tests.test_gene_view)
test_gene_view_summary_variants_download_group() (in module gene_view.tests.test_gene_view)
test_gene_view_summary_variants_query() (in module gene_view.tests.test_gene_view)
test_gene_view_summary_variants_query_group() (in module gene_view.tests.test_gene_view)
test_genome_hg19() (in module gpf_instance.tests.test_genome_view)
test_genome_hg38() (in module gpf_instance.tests.test_genome_view)
test_genome_other() (in module gpf_instance.tests.test_genome_view)
test_genotype_browser_download_columns_default() (in module studies.tests.test_study_config_genotype_browser_columns)
test_genotype_browser_download_columns_ext() (in module studies.tests.test_study_config_genotype_browser_columns)
test_genotype_browser_preview_columns_default() (in module studies.tests.test_study_config_genotype_browser_columns)
test_genotype_browser_preview_columns_ext() (in module studies.tests.test_study_config_genotype_browser_columns)
test_genotype_data_config_immutability() (in module studies.tests.test_study_wrapper)
test_get_bad_gene_set_collection_not_found() (in module gene_sets.tests.test_gene_sets_api)
test_get_case_insensitive_gene() (in module genomes_api.tests.test_gene_models_api)
test_get_chd8_transcripts() (in module genomes_api.tests.test_gene_models_api)
test_get_default_background_model() (in module enrichment_api.tests.test_enrichment_helper_simple)
test_get_default_background_model_default() (in module enrichment_api.tests.test_enrichment_helper_simple)
test_get_denovo_gene_set_not_found() (in module gene_sets.tests.test_gene_sets_api)
test_get_gene_gene_scores_db() (in module gene_scores.tests.test_gene_scores_db)
test_get_gene_set_collection_empty_query() (in module gene_sets.tests.test_gene_sets_api)
test_get_gene_set_download_synonymous_autism() (in module gene_sets.tests.test_gene_sets_api)
test_get_gene_set_download_synonymous_recurrent() (in module gene_sets.tests.test_gene_sets_api)
test_get_gene_set_download_synonymous_triple() (in module gene_sets.tests.test_gene_sets_api)
test_get_gene_symbols() (in module gene_profiles_api.tests.test_agp_api)
test_get_genes_by_score() (in module gene_scores.tests.test_gene_scores)
test_get_genomic_scores() (in module genomic_scores_api.tests.test_genomic_scores_api)
test_get_gpf_version() (in module gpf_instance.tests.test_version_api)
test_get_links() (in module gene_profiles_api.tests.test_agp_api)
test_get_main_gene_set_not_found() (in module gene_sets.tests.test_gene_sets_api)
test_get_nonexistant_gene_transcripts() (in module genomes_api.tests.test_gene_models_api)
test_get_person_sets_collection_stats() (in module person_sets_api.tests.test_person_sets_api)
test_get_person_sets_collection_stats_no_id() (in module person_sets_api.tests.test_person_sets_api)
test_get_person_sets_collection_stats_nonexistent() (in module person_sets_api.tests.test_person_sets_api)
test_get_selected_counting_models() (in module enrichment_api.tests.test_enrichment_helper_simple)
test_get_selected_counting_models_default() (in module enrichment_api.tests.test_enrichment_helper_simple)
test_get_selected_counting_models_default_with_counting() (in module enrichment_api.tests.test_enrichment_helper_simple)
test_get_selected_person_set_collections() (in module enrichment_api.tests.test_enrichment_helper_simple)
test_get_selected_person_set_collections_default() (in module enrichment_api.tests.test_enrichment_helper_simple)
test_get_statistic() (in module gene_profiles_api.tests.test_agp_api)
test_get_statistics() (in module gene_profiles_api.tests.test_agp_api)
test_get_study_background() (in module enrichment_api.tests.test_enrichment_helper_simple)
test_get_study_enrichment_config() (in module enrichment_api.tests.test_enrichment_helper_simple)
test_get_t4c8_score() (in module gene_scores.tests.test_gene_scores)
test_gpf_about_description() (in module gpf_instance.tests.test_version_api)
test_gpf_fixture() (in module enrichment_api.tests.test_enrichment_helper_simple)
test_gpf_main_description() (in module gpf_instance.tests.test_version_api)
test_histograms_beta() (in module measures_api.tests.test_measures_api)
test_inheritance_type_column() (in module studies.tests.test_response_transformer_columns)
test_is_denovo() (in module studies.tests.test_response_transformer_columns)
test_is_group_dataset() (in module studies.tests.test_study_wrapper)
test_is_group_study() (in module studies.tests.test_study_wrapper)
test_list_families_view() (in module family_api.tests.test_family_api)
test_list_families_view_nonexistent() (in module family_api.tests.test_family_api)
test_list_families_view_tag_filter() (in module family_api.tests.test_family_api)
test_list_families_view_tag_filter_multiple() (in module family_api.tests.test_family_api)
test_list_members_view() (in module family_api.tests.test_family_api)
test_list_members_view_nonexistent() (in module family_api.tests.test_family_api)
test_list_tags_view() (in module family_api.tests.test_family_api)
test_main_gene_set_not_found() (in module gene_sets.tests.test_gene_sets_api)
test_make_config() (in module studies.tests.test_study_wrapper)
test_measures_api_permissions() (in module measures_api.tests.test_measures_api)
test_measures_list_categorical() (in module measures_api.tests.test_measures_api)
test_measures_list_continuous() (in module measures_api.tests.test_measures_api)
test_measures_list_wrong_request() (in module measures_api.tests.test_measures_api)
test_member_details_view() (in module family_api.tests.test_family_api)
test_member_details_view_nonexistent() (in module family_api.tests.test_family_api)
test_nested_queries() (in module studies.tests.test_study_wrapper_queries)
test_person_set_collection_queries() (in module studies.tests.test_study_wrapper_person_sets)
test_pheno_measure_genotype_browser_columns() (in module studies.tests.test_pheno_measures_columns)
test_pheno_tool_api_permissions() (in module pheno_tool_api.tests.test_pheno_tool_api)
test_pheno_tool_download_valid_request() (in module pheno_tool_api.tests.test_pheno_tool_api)
test_pheno_tool_view_cnv_on_non_cnv_study() (in module pheno_tool_api.tests.test_pheno_tool_api)
test_pheno_tool_view_family_ids_filter() (in module pheno_tool_api.tests.test_pheno_tool_api)
test_pheno_tool_view_missense() (in module pheno_tool_api.tests.test_pheno_tool_api)
test_pheno_tool_view_missing_dataset() (in module pheno_tool_api.tests.test_pheno_tool_api)
test_pheno_tool_view_missing_measure() (in module pheno_tool_api.tests.test_pheno_tool_api)
test_pheno_tool_view_na_values() (in module pheno_tool_api.tests.test_pheno_tool_api)
test_pheno_tool_view_normalize() (in module pheno_tool_api.tests.test_pheno_tool_api)
test_pheno_tool_view_pheno_filter() (in module pheno_tool_api.tests.test_pheno_tool_api)
test_pheno_tool_view_query_no_limit() (in module pheno_tool_api.tests.test_pheno_tool_api)
test_pheno_tool_view_valid_request() (in module pheno_tool_api.tests.test_pheno_tool_api)
test_phenotype_attr_columns() (in module studies.tests.test_response_transformer_columns)
test_query_affected_status() (in module studies.tests.test_study_wrapper_queries)
test_query_all_variants() (in module studies.tests.test_study_wrapper_queries)
test_query_complex_query() (in module studies.tests.test_study_wrapper_queries)
test_query_effect_types_variants() (in module studies.tests.test_study_wrapper_queries)
test_query_family_filters() (in module studies.tests.test_study_wrapper_queries)
test_query_family_variants() (in module studies.tests.test_study_wrapper_queries)
test_query_gene_scores() (in module studies.tests.test_study_wrapper_queries)
test_query_gene_scores_formatting() (in module studies.tests.test_study_wrapper_queries)
test_query_gene_view_summary_variants_dataset() (in module gene_view.tests.test_gene_view)
test_query_gene_view_summary_variants_download_dataset() (in module gene_view.tests.test_gene_view)
test_query_gene_view_summary_variants_download_study() (in module gene_view.tests.test_gene_view)
test_query_gene_view_summary_variants_study() (in module gene_view.tests.test_gene_view)
test_query_inheritance_types() (in module studies.tests.test_study_wrapper_queries)
test_query_limit_variants() (in module studies.tests.test_study_wrapper_queries)
test_query_person_filters() (in module studies.tests.test_study_wrapper_queries)
test_query_present_in_child() (in module studies.tests.test_study_wrapper_queries)
test_query_present_in_parent() (in module studies.tests.test_study_wrapper_queries)
test_query_present_in_parent_and_present_in_child() (in module studies.tests.test_study_wrapper_queries)
test_query_present_in_parent_and_present_in_child_and_phenotypes() (in module studies.tests.test_study_wrapper_queries)
test_query_preview_have_pheno_column_values() (in module genotype_browser.tests.test_pheno_columns)
test_query_regions_variants() (in module studies.tests.test_study_wrapper_queries)
test_query_request_simple() (in module studies.tests.test_study_query_request)
test_query_sexes_variants() (in module studies.tests.test_study_wrapper_queries)
test_query_study_filters() (in module studies.tests.test_study_wrapper_queries)
test_query_unique_family_variants() (in module studies.tests.test_study_wrapper_queries)
test_query_variant_type_variants() (in module studies.tests.test_study_wrapper_queries)
test_query_with_pheno_filters() (in module genotype_browser.tests.test_pheno_filters)
test_regressions() (in module measures_api.tests.test_measures_api)
test_role_list() (in module measures_api.tests.test_measures_api)
test_scores_created() (in module gene_scores.tests.test_gene_scores)
test_search_gene_symbols() (in module genomes_api.tests.test_gene_models_api)
test_sentry_invalid_cookie() (in module sentry.tests.test_sentry)
test_sentry_missing_cookie() (in module sentry.tests.test_sentry)
test_sentry_missing_env() (in module sentry.tests.test_sentry)
test_sentry_valid_cookie() (in module sentry.tests.test_sentry)
test_serialize() (in module enrichment_api.tests.test_enrichment_serializer)
test_serialize_enrichment_result() (in module enrichment_api.tests.test_enrichment_serializer)
test_special_attr_columns() (in module studies.tests.test_response_transformer_columns)
test_special_attrs_formatting() (in module studies.tests.test_response_transformer_columns)
test_study_1() (in module enrichment_api.tests.test_t4c8_enrichment)
test_study_1_enrichment() (in module enrichment_api.tests.test_t4c8_enrichment)
test_study_1_enrichment_with_caching() (in module enrichment_api.tests.test_t4c8_enrichment)
test_study_2_query_inheritance_variants() (in module studies.tests.test_study_wrapper_queries)
test_study_with_phenotype_data() (in module studies.tests.test_pheno_measures_columns)
test_study_wrapper_download_columns_ext() (in module studies.tests.test_study_config_genotype_browser_columns)
test_study_wrapper_preview_columns_ext() (in module studies.tests.test_study_config_genotype_browser_columns)
test_summary_variant_ids() (in module studies.tests.test_study_wrapper_unique_variants_query)
test_t4c8_coding_len_background() (in module enrichment_api.tests.test_t4c8_enrichment)
test_t4c8_dataset() (in module studies.tests.test_study_wrapper)
test_t4c8_score_available() (in module gene_scores.tests.test_gene_scores)
test_t4c8_setup() (in module enrichment_api.tests.test_t4c8_enrichment)
test_t4c8_study_1() (in module studies.tests.test_study_wrapper)
test_t4c8_study_2() (in module studies.tests.test_study_wrapper)
test_transform_and_mode_family_tags_kwargs() (in module studies.tests.test_query_transformer_family_tags)
test_transform_complex_family_tags_kwargs() (in module studies.tests.test_query_transformer_family_tags)
test_transform_deselected_family_tags_kwargs() (in module studies.tests.test_query_transformer_family_tags)
test_transform_or_mode_family_tags_kwargs() (in module studies.tests.test_query_transformer_family_tags)
test_transform_parent_zygosity_with_neither() (in module studies.tests.test_query_transformer_present_in_child_and_parent)
test_transform_present_in_child_and_present_in_parent() (in module studies.tests.test_query_transformer_present_in_child_and_parent)
test_transform_present_in_child_and_present_in_parent_inheritance() (in module studies.tests.test_query_transformer_present_in_child_and_parent)
test_transform_present_in_child_and_present_in_parent_roles() (in module studies.tests.test_query_transformer_present_in_child_and_parent)
test_transform_selected_family_tags_kwargs() (in module studies.tests.test_query_transformer_family_tags)
test_unique_family_variants() (in module studies.tests.test_study_wrapper_unique_variants_query)
test_update_gpf_about_description_anonymous() (in module gpf_instance.tests.test_version_api)
test_update_gpf_main_description_anonymous() (in module gpf_instance.tests.test_version_api)
test_validate_gene_symbols() (in module genomes_api.tests.test_gene_models_api)
test_variant_reports() (in module common_reports_api.tests.test_common_reports_api)
test_variant_reports_full() (in module common_reports_api.tests.test_common_reports_api)
test_variant_reports_has_permissions() (in module common_reports_api.tests.test_common_reports_api)
test_variant_reports_permissions() (in module common_reports_api.tests.test_common_reports_api)
test_zygosity_gender() (in module studies.tests.test_study_wrapper_queries)
test_zygosity_roles_children() (in module studies.tests.test_study_wrapper_queries)
test_zygosity_roles_parents() (in module studies.tests.test_study_wrapper_queries)
test_zygosity_status() (in module studies.tests.test_study_wrapper_queries)
TestResult (class in gpf.tools.gpf_validation_runner)
TestStatus (class in gpf.tools.gpf_validation_runner)
TestSuite (class in gpf.tools.gpf_validation_runner)
text (gpf.pheno.common.MeasureType attribute)
time_fmt (gpf_web.default_settings.CustomFormatter attribute)
to_cshl_full() (gpf.variants.variant.VariantDesc method)
to_cshl_short() (gpf.variants.variant.VariantDesc method)
to_dict() (gpf.common_reports.common_report.CommonReport method)
(gpf.common_reports.denovo_report.DenovoReport method)
(gpf.common_reports.denovo_report.DenovoReportTable method)
(gpf.common_reports.denovo_report.EffectCell method)
(gpf.common_reports.denovo_report.EffectRow method)
(gpf.common_reports.family_counter.FamiliesGroupCounters method)
(gpf.common_reports.family_counter.FamilyCounter method)
(gpf.common_reports.family_report.FamiliesReport method)
(gpf.common_reports.people_counter.PeopleCounter method)
(gpf.common_reports.people_counter.PeopleCounters method)
(gpf.common_reports.people_counter.PeopleReport method)
(gpf.parquet.partition_descriptor.PartitionDescriptor method)
to_json() (gpf.gene_profile.statistic.GPStatistic method)
(gpf.genomic_scores.scores.ScoreDesc method)
(gpf.pedigrees.family.Family method)
(gpf.pedigrees.family.Person method)
(gpf.person_sets.person_sets.PersonSet method)
(gpf.person_sets.PersonSet method)
(gpf.pheno.pheno_data.Measure method)
to_name() (gpf.variants.attributes.Role static method)
(gpf.variants.attributes.Sex static method)
(gpf.variants.attributes.Status static method)
to_pylist() (gpf.parquet.partition_descriptor.Partition method)
to_record() (gpf.variants.family_variant.FamilyVariant method)
(gpf.variants.variant.SummaryAllele method)
(gpf.variants.variant.SummaryVariant method)
to_tsv() (gpf.pedigrees.loader.FamiliesLoader static method)
to_value() (gpf.variants.attributes.Role static method)
(gpf.variants.attributes.Sex static method)
(gpf.variants.attributes.Status static method)
to_xml_element() (gpf.tools.gpf_validation_runner.TestResult method)
(gpf.tools.gpf_validation_runner.TestSuite method)
TOMLDict (class in gpf.configuration.study_config_builder)
TOMLList (class in gpf.configuration.study_config_builder)
tool_id (gpf_instance.extension.GPFTool property)
total (gpf.person_sets.ChildrenStats property)
(gpf.person_sets.person_sets.ChildrenStats property)
transform_attribute_query_to_function() (in module gpf.query_variants.attribute_queries)
transform_attribute_query_to_sql_expression() (in module gpf.query_variants.attribute_queries)
transform_attribute_query_to_sql_expression_schema1() (in module gpf.query_variants.attribute_queries)
transform_cli_args() (in module gpf.pheno.pheno_import)
transform_gene_view_summary_variant() (studies.response_transformer.ResponseTransformer method)
(studies.study_wrapper.ResponseTransformerProtocol method)
transform_gene_view_summary_variant_download() (studies.response_transformer.ResponseTransformer method)
(studies.study_wrapper.ResponseTransformerProtocol method)
transform_kwargs() (studies.query_transformer.QueryTransformer method)
(studies.study_wrapper.QueryTransformerProtocol method)
transform_ps_query_to_attribute_queries() (gpf.person_sets.person_sets.PersonSetCollection method)
(gpf.person_sets.PersonSetCollection method)
transform_roles_to_single_role_string() (gpf.query_variants.base_query_variants.QueryVariants static method)
translate() (gpf.pedigrees.layout.Layout method)
transmission_type (gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.variant.SummaryAllele property)
(gpf.variants.variant.SummaryVariant property)
TransmissionType (class in gpf.variants.attributes)
transmitted (gpf.variants.attributes.TransmissionType attribute)
TRIO (gpf.pedigrees.family.FamilyTag attribute)
trio_study() (in module studies.tests.test_study_config_genotype_browser_columns)
trios (gpf.pedigrees.family.Family property)
TripleCriteria (class in gpf.gene_sets.denovo_gene_sets_config)
try_solve() (gpf.pedigrees.pedigrees.SandwichSolver static method)
tvalues (gpf.pheno.utils.lin_regress.LinearRegression property)
type (gpf.import_tools.import_tools.Bucket attribute)
TYPE_DISPLAY_NAME (gpf.variants.core.Allele attribute)
U
U (gpf.variants.attributes.Sex attribute)
ultra_rare() (gpf.query_variants.sql.schema2.sql_query_builder.SqlQueryBuilder static method)
unaffected (gpf.variants.attributes.Status attribute)
UNAFFECTED_DAD (gpf.pedigrees.family.FamilyTag attribute)
UNAFFECTED_MOM (gpf.pedigrees.family.FamilyTag attribute)
UNAFFECTED_PRB (gpf.pedigrees.family.FamilyTag attribute)
UNAFFECTED_SIB (gpf.pedigrees.family.FamilyTag attribute)
undefined (gpf.variants.attributes.Zygosity attribute)
unix_timestamp (gpf.pheno.common.ImportManifest attribute)
unknown (gpf.variants.attributes.Inheritance attribute)
(gpf.variants.attributes.Role attribute)
(gpf.variants.attributes.TransmissionType attribute)
unregister_genotype_data() (gpf.studies.variants_db.VariantsDb method)
unset_tag() (gpf.pedigrees.family.Family method)
(gpf.pedigrees.family.Person method)
(in module gpf.pedigrees.family_tag_builder)
unspecified (gpf.enrichment_tool.event_counters.EnrichmentResult attribute)
(gpf.enrichment_tool.event_counters.EventCountersResult attribute)
(gpf.enrichment_tool.event_counters.EventsResult attribute)
(gpf.enrichment_tool.event_counters.VariantEventsResult attribute)
(gpf.person_sets.ChildrenBySex attribute)
(gpf.person_sets.ChildrenStats attribute)
(gpf.person_sets.person_sets.ChildrenBySex attribute)
(gpf.person_sets.person_sets.ChildrenStats attribute)
(gpf.variants.attributes.Sex attribute)
(gpf.variants.attributes.Status attribute)
update_attribute_query_with_compounds() (in module gpf.query_variants.attribute_queries)
update_attributes() (gpf.variants.family_variant.FamilyAllele method)
(gpf.variants.variant.SummaryAllele method)
(gpf.variants.variant.SummaryVariant method)
update_cache() (gpf.gene_sets.denovo_gene_sets_db.DenovoGeneSetsDb method)
update_gps_with_values() (gpf.gene_profile.db.GeneProfileDBWriter method)
update_study_config() (in module gpf.testing.import_helpers)
url_to_pyarrow_fs() (in module gpf.parquet.helpers)
use_bit_and_function() (gpf.duckdb_storage.duckdb_variants.DuckDbQueryDialect static method)
(gpf.query_variants.sql.schema2.base_query_builder.Dialect static method)
use_ssl (gpf.duckdb_storage.duckdb_storage_config.DuckDbS3Conf attribute)
(gpf.duckdb_storage.duckdb_storage_config.DuckDbS3ParquetConf attribute)
user_queries
module
user_queries.migrations
module
user_queries.migrations.0001_initial
module
users_api
module
users_api.management
module
users_api.management.commands
module
users_api.management.commands.user_set_name
module
users_api.management.commands.user_setpasswd
module
users_api.management.commands.users_remove
module
users_api.migrations
module
users_api.migrations.0001_initial
module
users_api.migrations.0002_auto_20190424_0751
module
users_api.migrations.0003_authenticationlog
module
users_api.migrations.0004_resetpasswordcode_setpasswordcode_and_more
module
users_api.migrations.0005_gpuserstate
module
users_api.tests
module
utils
module
utils.authentication
module
utils.datasets
module
utils.email_regex
module
utils.expand_gene_set
module
utils.gene_sets
module
utils.logger
module
utils.pagination
module
utils.password_requirements
module
utils.query_params
module
utils.streaming_response_util
module
utils.testing
module
V
validate_and_normalize_config() (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage class method)
(gpf.genotype_storage.genotype_storage.GenotypeStorage class method)
(gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage class method)
(gpf.parquet_storage.storage.ParquetGenotypeStorage class method)
validate_config() (gpf.configuration.gpf_config_parser.GPFConfigParser static method)
validate_existing_path() (in module gpf.configuration.utils)
validate_path() (in module gpf.configuration.utils)
validation_rules (gpf.configuration.gpf_config_parser.GPFConfigValidator attribute)
VALIDATION_SCHEMA (gpf.duckdb_storage.duckdb_legacy_genotype_storage.DuckDbLegacyStorage attribute)
(gpf.inmemory_storage.inmemory_genotype_storage.InmemoryGenotypeStorage attribute)
(gpf.parquet_storage.storage.ParquetGenotypeStorage attribute)
value_max_len (gpf.pheno.common.InferenceConfig attribute)
value_type (gpf.pheno.common.InferenceConfig attribute)
(gpf.pheno.prepare.measure_classifier.InferenceReport attribute)
values (gpf.person_sets.person_sets.PersonSetConfig attribute)
(gpf.person_sets.PersonSetConfig attribute)
values() (gpf.pedigrees.families_data.FamiliesData method)
values_domain (gpf.pheno.prepare.measure_classifier.InferenceReport attribute)
variant_in_member_fpids (gpf.variants.family_variant.FamilyAllele property)
variant_in_members (gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
variant_in_roles (gpf.variants.family_variant.FamilyAllele property)
variant_in_sexes (gpf.variants.family_variant.FamilyAllele property)
variant_in_statuses (gpf.variants.family_variant.FamilyAllele property)
variant_to_variant_type() (in module gpf.variants_loaders.raw.flexible_variant_loader)
variant_transformer() (studies.response_transformer.ResponseTransformer method)
(studies.study_wrapper.ResponseTransformerProtocol method)
variant_type (gpf.variants.variant.SummaryAllele property)
variant_types (gpf.variants.variant.SummaryVariant property)
VariantDesc (class in gpf.variants.variant)
VariantDetails (class in gpf.variants.variant)
VariantEvent (class in gpf.enrichment_tool.genotype_helper)
VariantEventsResult (class in gpf.enrichment_tool.event_counters)
variants_filenames (gpf.variants_loaders.dae.loader.DaeTransmittedLoader property)
(gpf.variants_loaders.raw.loader.VariantsLoader property)
(gpf.variants_loaders.vcf.loader.VcfLoader property)
variants_loader_annotate_and_save() (in module gpf.inmemory_storage.annotation_serialization)
variants_loader_load_annotation() (in module gpf.inmemory_storage.annotation_serialization)
VariantsDataSerializer (class in gpf.parquet.schema2.serializers)
VariantsDb (class in gpf.studies.variants_db)
VariantsGenotypesLoader (class in gpf.variants_loaders.raw.loader)
VariantsLoader (class in gpf.variants_loaders.raw.loader)
VariantsLoaderBatchSource (class in gpf.parquet.schema2.processing_pipeline)
VariantsLoaderDecorator (class in gpf.variants_loaders.raw.loader)
VariantsLoaderSource (class in gpf.parquet.schema2.processing_pipeline)
VariantsParquetWriter (class in gpf.parquet.schema2.variants_parquet_writer)
VariantsParquetWriterDeprecated() (in module gpf.parquet.schema2.parquet_io)
vcf (gpf.testing.import_helpers.StudyInputLayout attribute)
vcf2cshl() (in module gpf.variants.variant)
vcf_import() (in module gpf.testing.import_helpers)
vcf_liftover_main() (in module gpf.tools.liftover_tools)
vcf_study() (in module gpf.testing.import_helpers)
VcfFamiliesGenotypes (class in gpf.variants_loaders.vcf.loader)
vcffile_chromosomes() (in module gpf.variants_loaders.vcf.loader)
VCFLiftoverTool (class in gpf.tools.liftover_tools)
VcfLoader (class in gpf.variants_loaders.vcf.loader)
VcfSerializer (class in gpf.variants_loaders.vcf.serializer)
W
WDAEAbstractStudy (class in studies.study_wrapper)
WDAEConfig (class in gpf_instance.apps)
WdaePageNumberPagination (class in utils.pagination)
WDAEStudy (class in studies.study_wrapper)
WDAEStudyGroup (class in studies.study_wrapper)
wgpf_fixture() (in module studies.tests.test_study_group_person_sets_queries)
wgpf_instance() (in module studies.tests.test_study_wrapper_person_sets)
(in module studies.tests.test_study_wrapper_unique_variants_query)
WHERE (gpf.query_variants.sql.schema2.base_query_builder.BaseQueryBuilder attribute)
work_dir (gpf.import_tools.import_tools.ImportProject property)
(gpf.pheno.common.PhenoImportConfig attribute)
worst_effect (gpf.variants.variant.SummaryAllele property)
write() (gpf.parquet.schema2.variants_parquet_writer.VariantsParquetWriter method)
write_descriptions() (in module gpf.pheno.pheno_import)
write_new_meta() (in module gpf.parquet.schema2.annotate_schema2_parquet)
write_reports_to_parquet() (in module gpf.pheno.pheno_import)
write_results() (in module gpf.pheno.pheno_import)
write_summary_variant() (gpf.parquet.schema2.variants_parquet_writer.VariantsParquetWriter method)
write_to_db() (gpf.pheno.common.ImportManifest static method)
write_to_parquet() (in module gpf.pheno.pheno_import)
X
x (gpf.pedigrees.layout.Point attribute)
X (gpf.variants.attributes.GeneticModel attribute)
X_broken (gpf.variants.attributes.GeneticModel attribute)
x_center (gpf.pedigrees.layout.IndividualWithCoordinates property)
Y
y (gpf.pedigrees.layout.Point attribute)
y_center (gpf.pedigrees.layout.IndividualWithCoordinates property)
year (gpf.studies.study.GenotypeData property)
yellow (gpf_web.default_settings.CustomFormatter attribute)
Z
Zygosity (class in gpf.variants.attributes)
zygosity_in_roles (gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
zygosity_in_sexes (gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
zygosity_in_status (gpf.variants.family_variant.FamilyAllele property)
(gpf.variants.family_variant.FamilyVariant property)
ZygosityQuery (class in gpf.query_variants.sql.schema2.sql_query_builder)